Any process involved in maintaining the methylation state of a nucleotide sequence. [PMID:11898023]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
Repression of transcription by methylation of DNA, leading to the formation of heterochromatin. [GOC:mah]
Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin. [GOC:mah, PMID:10219245]
The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. [GOC:ems, ISBN:0198506732]
The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure. [GOC:go_curators]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria. [GOC:ai]
A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell. [GOC:add]
A defense response that is mediated by cells. [GOC:ebc]
Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell. [GOC:bf]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing. [GOC:clt, PMID:12730603]
The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. [GOC:dph, GOC:tb]
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body. [GOC:mah, PMID:17429074]
Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening. [GOC:krc, PMID:15225542, PMID:15225544]
Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA. [GOC:dgf, PMID:20802481]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. [GOC:kmv, SO:0000234]
A complex of five proteins, designated NELF-A, -B, -C, -D, and -E in human, that can physically associate with RNP polymerase II to induce transcriptional pausing. [PMID:12612062]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II. [GOC:mah, GOC:txnOH]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl, PMID:12115731]
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with the enzyme histone acetyltransferase. [GOC:bf]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH]
Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery. [GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. [GOC:txnOH]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. [GOC:txnOH]
Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. [GOC:mah, GOC:pr, ISBN:0815316194]
A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments. [ISBN:0815316194]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Any process that modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Formation of a microspike, a dynamic, actin-rich projection extending from the surface of a migrating animal cell. [ISBN:0815316194, PMID:11429692, PMID:12153987, PMID:19095735]
Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell. [GOC:mah, ISBN:0815316194]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:mah]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle. [ISBN:0198506732]
Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. [GOC:ai]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP. [EC:1.1.1.-, GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH + H+. [EC:1.1.1.41]
Interacting selectively and non-covalently with magnesium (Mg) ions. [GOC:ai]
The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. [GOC:dph, GOC:ef, GOC:jid, GOC:lm, GOC:mtg_muscle]
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the peroxisomal membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:mah]
The lipid bilayer surrounding a peroxisome. [GOC:mah]
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria. [PMID:12588810]
Any process that modulates the volume of a peroxisome, a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. [GOC:jl]
The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments. [GOC:mah, PMID:11687502, PMID:14754507]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. [GOC:mah]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain. [GOC:mtg_sensu, GOC:vw, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. [GOC:mtg_electron_transport, ISBN:0716720094]
A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. [GOC:mtg_electron_transport]
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor. [GOC:das, GOC:jl, ISBN:0140513590]
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
The transfer of electrons from succinate to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex II. [ISBN:0716731363]
The chemical reactions and pathways involving succinate, also known as butanedioate or ethane dicarboxylate, the dianion of succinic acid. Succinate is an important intermediate in metabolism and a component of the TCA cycle. [ISBN:0198506732]
A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle. [ISBN:0198506732]
Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. [GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. [ISBN:0198506732]
Catalysis of the reaction: succinate + ubiquinone = fumarate + ubiquinol. [EC:1.3.5.1, RHEA:13716]
Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor. [EC:1.3.99.1, GOC:kd]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma. [CL:0000545, GOC:ebc]
The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. [CL:0000782, GOC:jl]
An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin. [GOC:add, ISBN:0781735149]
The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52). [GOC:bf, GOC:mg2, GOC:signaling, GOC:vs, PMID:11239468, PMID:15140882]
Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-beta production. [GOC:mah]
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:15771591, PMID:15928678]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH]
A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. [GOC:bf, GOC:mah, PMID:9407099]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus. [GOC:sl]
The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. [GOC:bf, GOC:jl, PMID:12773372, Reactome:REACT_13696.1]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. [GOC:txnOH]
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). [GOC:go_curators]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process in which a relatively unspecialized cell acquires the specialized features of a midbrain dopaminergic neuron. [GO_REF:0000086, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:17331494, PMID:19122665]
Any Wnt signaling pathway, planar cell polarity pathway that is involved in axon guidance. [GO_REF:0000060, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:21106844, PMID:23517308]
The process in which the migration of an axon growth cone of a commissural neuron is directed to its target in the brain in response to a combination of attractive and repulsive cues. [GOC:BHF, GOC:mah]
The directed movement of a motile cell or organism towards a lower concentration of a chemical. [GOC:ai, GOC:bf, GOC:isa_complete]
Any process that stops, prevents, or reduces the frequency, rate or extent of axon extension involved in axon guidance. [GOC:devbiol]
The process in which the anatomical structures of the skeleton are generated and organized. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb]
The process in which a dopaminergic neuron growth cone is directed to a specific target site in response to a repulsive chemical cue. [GOC:bf, GOC:PARL, PMID:21106844, PMID:23517308]
The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:mah]
The process in which a relatively unspecialized cell acquires specialized features of a neuron. [GOC:mah]
The process whose specific outcome is the progression of the corpus callosum over time, from its formation to the mature structure. The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provide communication between the right and left cerebral hemispheres. [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state. [GOC:dph, GOC:go_curators, PMID:11532397]
The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues. [ISBN:0878932437]
De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon. [GOC:dph, GOC:jid, GOC:pg, GOC:pr, ISBN:0198506732]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity. [GOC:go_curators]
Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling. [GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with the frizzled (fz) receptor. [GOC:ceb, PR:000001315]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. [GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:mah]
Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell. [GOC:ai, GOC:jid, GOC:mah]
The process in which the developmental fate of a cell becomes restricted such that it will develop into a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. [CL:0000056, GOC:dph, GOC:mtg_muscle]
A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl]
Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli. [PMID:9751757]
The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine. [GOC:jl, ISBN:0198506732]
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. [GOC:jid, UBERON:0002048]
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. [GOC:mah]
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. [ISBN:0198506732]
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. [GOC:dgh, ISBN:0198506732]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl, PMID:12115731]
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Any process that modulates the frequency or rate of heart contraction. [GOC:dph, GOC:tb, PMID:10358008]
The reorganization or renovation of existing blood vessels. [GOC:hjd]
The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin. [GOC:add, ISBN:068340007X]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:hjd]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with the enzyme histone acetyltransferase. [GOC:bf]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH]
A protein complex that regulates RNA degradation by the exosome complex. In Saccharomyces the complex has a heterotetrameric stoichiometry consisting of one copy each of Ski2p and Ski3 and two copies of Ski8p. [GOC:mcc, PMID:10744028, PMID:15703439, PMID:16043509, PMID:18042677]
The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction. [PMID:12769863]
The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix. [EC:3.6.1.3, GOC:jl]
Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix. [GOC:jl, GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis. [GOC:go_curators]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The maintenance of the apicobasal polarity of an epithelial cell. [GOC:bf]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, ISBN:0815316194]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
A ubiquitin ligase complex that catalyzes linear head-to-tail polyubiquitin conjugation on its targets. In human the complex consists of RBCK1, RNF31 and SHARPIN, and has an MW of approximately 600 kDa, suggesting a heteromultimeric assembly of its subunits. LUBAC stands for Linear Ubiquitin Chain Assembly Complex. [GOC:sp, PMID:17006537, PMID:19136968, PMID:21455180]
Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway. [GOC:mtg_apoptosis]
A protein ubiquitination process in which a linear polymer of ubiquitin, formed by the amino-terminal methionine (M1) of one ubiquitin molecule and by the carboxy-terminal glycine (G76) of the next, is added to a protein. [GOC:jsg, GOC:sp, PMID:21455173, PMID:21455180, PMID:21455181]
Any process that decreases the rate, frequency or extent of a necroptotic process, a necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors. [GOC:BHF, GOC:dph, GOC:mtg_apoptosis, GOC:tb]
Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB. [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030]
A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell. [GOC:add]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:jl, ISBN:0198506732]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. [GOC:dph, GOC:rl, GOC:tb]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation. [GOC:ecd]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. [GOC:BioGRID, GOC:jh2, PMID:9635407]
A conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. [PMID:11687631, PMID:11742990, PMID:11805083, PMID:12488447, PMID:18508253, PMID:18838538]
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone. [GOC:ai, GOC:pr]
Repression of transcription of telomeric DNA by altering the structure of chromatin. [PMID:10219245]
Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein. [PMID:12086618]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A process in which a zinc II ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:BHF, GOC:mah]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of zinc (Zn II) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Enables the transfer of metal ions from one side of a membrane to the other. [GOC:ai]
Enables the transfer of zinc (Zn) ions from one side of a membrane to the other. [GOC:dgf]
A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids. [GOC:BHF, GOC:mah, PMID:16373184]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. [PMID:16645198, PMID:20044567]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that modulates the frequency, rate or extent of acid-sensing ion channel activity. [GOC:TermGenie]
Any process that increases the frequency, rate or extent of the process of directing proteins towards a membrane, usually using signals contained within the protein. [GOC:tb]
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of a multi-organism process in which a virus is a participant. [GOC:bf, GOC:jl]
A process in which a host organism activates or increases the frequency, rate or extent of  viral genome replication. [GOC:jl]
Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. [GOC:mah]
Interacting selectively and non-covalently with an RNA polymerase molecule or complex. [GOC:BHF, GOC:mah, GOC:txnOH]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell. [ISBN:0716731363]
A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. [http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm, ISBN:0198506732]
Any process that modulates the frequency, rate or extent of keratinocyte differentiation. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of an epidermal cutaneous structure. [GOC:mah]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2). [CHEBI:18421, GOC:jl]
The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species. [CHEBI:18421, GOC:jl]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:hjd]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with copper (Cu) ions. [GOC:ai]
Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide. [EC:1.15.1.1, GOC:vw, PMID:15064408]
A protein complex consisting of cyclin E1 and cyclin-dependent kinase 2 (CDK2). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner. [GOC:so, PMID:15935619, PR:000026745]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner. [GOC:krc, PMID:11602261]
Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. [GO_REF:0000058, GOC:TermGenie, GOC:vw]
A process of chromosome organization that is involved in a meiotic cell cycle. [GOC:mah]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state. [GOC:dph, GOC:go_curators, PMID:11532397]
The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Synapsis begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete. [GOC:mtg_cell_cycle, PMID:22582262, PMID:23117617]
The process of introducing a phosphate group on to a protein. [GOC:hb]
The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action. [ISBN:071673706X, ISBN:0815316194]
Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences. [GOC:BHF, GOC:BHF_telomere, GOC:elh, GOC:rl, PMID:11092831]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated. [GOC:mtg_cell_cycle]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
Modulates the activity of a cyclin-dependent protein serine/threonine kinase, enzymes of the protein kinase family that are regulated through association with cyclins and other proteins. [GOC:pr, GOC:rn, PMID:7877684, PMID:9442875]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
A protein complex that functions downstream of the MRN complex to promote DNA repair and the G2/M checkpoint. The SOSS complex associates with single-stranded DNA at DNA lesions and is composed of SOSS-B (SOSS-B1/OBFC2B or SOSS-B2/OBFC2A), SOSS-A/INTS3 and SOSS-C/C9orf80. [PMID:19683501]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. [PMID:12509526]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
The ring-like, filamentous structure located at the distal end of the midpiece of the sperm flagellum; the annulus is thought to form a diffusion barrier between the midpiece and the principal piece and serve as a stabilizing structure for tail rigidity. [GOC:cjm, MP:0009834]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A protein complex containing septins.  Typically, these complexes contain multiple septins and are oligomeric. [GOC:mah, PMID:15385632]
A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis. [ISBN:0815316194]
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. [ISBN:0198547684]
Any process involved in the controlled movement of a sperm cell. [GOC:cilia, GOC:krc]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
Any process that modulates the frequency, rate or extent of T cell differentiation in the thymus. [GOC:add, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The process of removing one or more phosphate groups from a phosphorylated lipid, any member of a group of substances soluble in lipid solvents but only sparingly soluble in aqueous solvents. [ISBN:0198506732]
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester. [ISBN:0198506732]
Catalysis of the reaction: a phospholipid + H2O = a lipid + phosphate. [GOC:jl]
Catalysis of the reaction: a 1,2-diacylglycerol 3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate. [EC:3.1.3.4, GOC:pr]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. [GOC:go_curators]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits. [GOC:go_curators]
Catalysis of the reaction: (R)-NADHX = (S)-NADHX. [PMID:21994945]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. [ISBN:0198506732]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms. [GOC:dph]
The process in which a nerve invades a tissue and makes functional synaptic connection within the tissue. [GOC:dph, GOC:sart]
The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin. [GOC:dgh, GOC:dph, PMID:11487378]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:go_curators]
The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein. [GOC:go_curators]
The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GOC:mah]
An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700). [GOC:PO_curators]
The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues. [CL:0000100, GOC:pr, ISBN:0878932437]
De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon. [GOC:dph, GOC:jid, GOC:pg, GOC:pr, ISBN:0198506732]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues. [GOC:BioGRID, GOC:dph, GOC:mah, GOC:tb, PMID:22863777]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate. [ISBN:0198506732]
The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate. [GOC:ai]
Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. [EC:2.7.4.6]
A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A histone acetyltransferase complex that has histone H3 acetyltransferase and coactivator activities. Subunits of the human complex include MYST3/MOZ, MYST4/MORF, ING5, EAF6 and one of BRPF1, BRD1/BRPF2 and BRPF3. [PMID:18794358]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection. [GOC:ma, PMID:10944585]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. [GOC:elh]
A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest. [GOC:BHF]
Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. [GOC:dph, GOC:jid]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The modification of histone H3 by the addition of an acetyl group. [GOC:jl]
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. [GOC:add, ISBN:0781735149]
The modification of a histone by the addition of an acetyl group. [GOC:ai]
The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. [GOC:ai]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA. [GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor). [GOC:jl]
Catalysis of the transfer of an acetyl group to an acceptor molecule. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone. [EC:2.3.1.48]
Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
Any process that increases the concentration of calcium ions in the cytosol that occurs as part of a PLC-activating G-protein coupled receptor signaling pathway. G-protein-activated PLC hydrolyses phosphatidylinositol-bisphosphate (PIP2) to release diacylglycerol (DAG) and inositol trisphosphate (IP3). IP3 then binds to calcium release channels in the endoplasmic reticulum (ER) to trigger calcium ion release into the cytosol. [GOC:ai, GOC:signaling]
The series of molecular signals generated as a consequence of a receptor binding to an extracellular purine nucleotide and transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. [GOC:BHF, PMID:9755289]
Any process that activates or increases the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
Combining with a purine nucleotide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:mah, PMID:9755289]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1). [PMID:15571813, PMID:15688063]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage. [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, GOC:TermGenie, PMID:15314165]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GOC:jl]
The removal of the ubiquitin group from a monoubiquitinated protein. [GOC:bf]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. [GOC:mah]
Any process that activates or increases the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
The removal of one or more ubiquitin groups from a protein. [GOC:ai]
Any cell cycle regulatory process that decreases the rate or extent of progression of a cell from G2 to M phase of the mitotic cell cycle. [GOC:mtg_cell_cycle]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein. [GOC:go_curators]
In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. [ISBN:0815316194]
Interacting selectively and non-covalently with a WD40 repeat domain of a protein. The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Several of these repeats are combined to form a type of protein domain called the WD domain. [GOC:yaf, InterPro:IPR017986]
Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin. [EC:3.4.19.12, GOC:bf, GOC:ka]
Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein. [GOC:jh2, ISBN:0120793709]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/]
A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle. [ISBN:0198547684]
A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
Any process that modulates the frequency, rate or extent of the formation of a daughter centriole of an existing centriole. [GOC:ai]
A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding. [GOC:bf, GOC:mah, PMID:12381728, PMID:15579462]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:dos, GOC:vw]
A process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. [GOC:dph, GOC:ef]
Any process that modulates the potential difference across a post-synaptic membrane. [GOC:dph, GOC:ef]
A organ system process carried out by any of the organs or tissues of neurological system. [GOC:ai, GOC:mtg_cardio]
The process whose specific outcome is the progression of the muscle fiber over time, from its formation to the mature structure. In skeletal muscle, fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. [GOC:dph, GOC:jid, GOC:lm, GOC:mtg_muscle]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
Any process that results in a change in the behavior of an organism as a result of a nicotine stimulus. [GOC:bf, ISBN:0198506732]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nicotine stimulus. [CHEBI:17688, GOC:bf, GOC:ef, ISBN:0198506732, ISBN:0582227089]
The process of communication from a neuron to a muscle, across a synapse. [GOC:jl, MeSH:D009435]
The process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse using the neurotransmitter acetylcholine. [GOC:kmv, GOC:pr, Wikipedia:Cholinergic]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. [GOC:ef, GOC:mtg_muscle, ISBN:0198506732]
The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
A process which results in the assembly, arrangement of constituent parts, or disassembly of a postsynaptic membrane, the specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). [GOC:dph, GOC:pr]
Interacting selectively and non-covalently with acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. [GOC:ai]
Selectively enables the transmembrane transfer of a cation by a channel that opens upon binding acetylcholine. [GOC:mah, PMID:2466967]
Combining with acetylcholine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:jl, GOC:signaling]
Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. [GOC:mtg_transport, ISBN:0815340729, TC:1.-.-.-.-]
Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs. [GOC:mah, PMID:12045094]
A ribonuclease P complex located in the nucleolus of a eukaryotic cell, where it catalyzes the 5' endonucleolytic cleavage of precursor tRNAs to yield mature tRNAs. Eukaryotic nucleolar ribonuclease P complexes generally contain a single RNA molecule that is necessary but not sufficient for catalysis, and several protein molecules. [GOC:mah, PMID:12045094]
A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family, and cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication. [GOC:sgd_curators, PMID:10690410, PMID:14729943, PMID:7510714]
The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. [GOC:dph, GOC:tb]
The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. [GOC:jl, PMID:12533506]
Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. [GOC:mah]
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. [GOC:curators]
Interacting selectively and non-covalently with the RNA subunit of ribonuclease P. [GOC:pg, PMID:11455963]
Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. [GOC:mah, ISBN:0198547684]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor. [EC:3.1.26.5]
Catalysis of the site-specific cleavage of RNA by a catalytic RNA-mediated mechanism; substrates include the A3 site in the ITS1 of pre-rRNA. [PMID:17881380]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents or reduces the frequency, rate or extent of ubiquitin protein ligase activity. [GO_REF:0000059, GOC:dph, GOC:tb, GOC:TermGenie, PMID:26216882]
Any process that modulates the rate, frequency, or extent of the spindle checkpoint, a cell cycle checkpoint that delays the metaphase/anaphase transition until the spindle is correctly assembled and oriented, and chromosomes are attached to the spindle. [GOC:ascb_2009, GOC:dph, GOC:tb]
The removal of one or more ubiquitin groups from a protein. [GOC:ai]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein. [GOC:go_curators]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin. [EC:3.4.19.12, GOC:bf, GOC:ka]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein. [GOC:jh2, ISBN:0120793709]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Any process that modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:mah]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation). [ISBN:0198506732]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of JUN kinase activity. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade. [GOC:mah]
A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G2/M transition of the cell cycle in response to DNA damage. [GOC:mtg_cell_cycle]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
The process of introducing a phosphate group on to a protein. [GOC:hb]
An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell. [GOC:bf, GOC:mtg_signaling_feb11, PMID:20811974, PMID:9561267]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [EC:2.7.11.13, GOC:bf, GOC:mah]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
A highly conserved protein complex comprised of two ATP-dependent DNA helicases (Rvb1p and Rvb2p in yeast, Pontin52 and Reptin52 in humans), Pih1p in yeast or PIH1D1 in humans, and Tah1 in yeast or RPAP3 in humans. The complex associates with Hsp90 and is thought to have a role in assembly of large protein or protein/nucleic acid complexes. In this role it is involved in multiple processes such as box C/D snoRNP biogenesis, phosphatidylinositol-3 kinase-related protein kinase (PIKK) signaling, RNA polymerase II assembly, and others. [GOC:mcc, PMID:15766533, PMID:21925213]
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue. [GOC:mah, ISBN:0815316194]
A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell. [GOC:cilia, GOC:dgh, GOC:kmv, PMID:17009929, PMID:20144998, PMID:22118931]
Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity. [ISBN:0815316194]
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. [GOC:bf, GOC:cilia, ISBN:0198547684]
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. [ISBN:0879693568]
Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains. [GOC:cilia, GOC:hla, GOC:krc, GOC:mah, PMID:12600311]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The aggregation, arrangement and bonding together of a set of components to form a non-motile cilium. [GO_REF:0000079, GOC:cilia, GOC:kmv, GOC:TermGenie, PMID:14521833, PMID:14521834]
The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure. [GOC:mtg_heart]
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2]
Any process that activates or increases the frequency, rate or extent of smoothened signaling. [GOC:go_curators]
The directed movement of large protein complexes along microtubules from the tip of a cilium (also called flagellum) toward the cell body, mediated by motor proteins. [GOC:BHF, GOC:cilia]
The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions). [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=forebrain]
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping. [GOC:bf, GOC:jl, ISBN:0395825172]
The process in which a relatively unspecialized cell acquires specialized features of a neuron. [GOC:mah]
The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869]
Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein. [GOC:curators, GOC:jl, GOC:jsg]
The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism. [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
Any process in which a protein is transported to, or maintained in, a specific location such that it is distributed asymmetrically. [GOC:ma]
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:jid, UBERON:0000948]
The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry. [GOC:dph, GOC:jid]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus. [GOC:dph, GOC:jl, GOC:mah]
A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components.  Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. [GOC:cjm, ISBN:0815316194]
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction. [EC:3.6.1.3, GOC:jl]
Catalysis of movement along a microtubule toward the minus end, coupled to the hydrolysis of ATP. [EC:3.6.4.5, GOC:mah, GOC:vw]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP). [GOC:mah, ISBN:0815316194]
Any vesicle that is part of the extracellular region. [GO_REF:0000064, GOC:pm, GOC:TermGenie, PMID:24769233]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The transport of an inorganic cation across a membrane and against an electrochemical gradient, using energy from ATP hydrolysis. [GOC:BHF]
A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:mah]
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. [GOC:ceb, GOC:mah]
The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins. [GOC:go_curators, Pfam:PF00595]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Ca2+(cis) = ADP + phosphate + Ca2+(trans). [EC:3.6.3.8]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
The evagination of an endoplasmic reticulum membrane, resulting in formation of a COPII-coated vesicle. [GOC:ascb_2009, GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of viral genome replication. [GOC:ai]
The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation. [GOC:mah, PMID:12042763]
The process in which a virus effects a change in the structure or processes of its host organism. [GOC:bf, GOC:jl, ISBN:0781718325, UniProtKB-KW:KW-0945]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum. [GOC:dph, GOC:jl, GOC:mah]
The conversion of a specific protein, possessing protein kinase and endoribonuclease activities, to an active form as a result of signaling via the unfolded protein response. [GOC:dph, GOC:mah, GOC:tb, PMID:12042763]
The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi. [GOC:ascb_2009, GOC:dph, GOC:jp, GOC:tb, ISBN:0716731363]
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. [GOC:ceb, GOC:mah]
Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin. [GOC:krc]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with the FFAT motif, a short motif containing diphenylalanine in an acidic tract that targets proteins to the cytosolic surface of the ER and to the nuclear membrane by binding directly to members of the VAP (VAMP-associated protein) protein family. [PMID:12727870, PMID:15455074, PMID:16004875]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Any process that activates or increases the frequency, rate or extent of NLRP3 inflammasome complex assembly. [GOC:TermGenie]
Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response. [GOC:TermGenie]
The regulated release of interleukin-18 from a cell. [GOC:BHF, GOC:mah, http://www.copewithcytokines.de/cope.cgi?key=interleukins]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far. [GOC:mah, PR:000000017]
The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits. [GOC:go_curators]
The regulated release of interleukin 1 beta from a cell. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. [GOC:ebc]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. [GOC:mtg_electron_transport]
Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. [GOC:ai]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex. An example of this component is found in Mus musculus. [GOC:jl, GOC:mtg_sensu, GOC:rb, PMID:10854779]
A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex. [GOC:rb, PMID:10806206]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core. [GOC:rb, http://en.wikipedia.org/wiki/Proteasome]
The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells. [GOC:ai, GOC:dph, GOC:tb]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the hydrolysis of internal peptide bonds in a polypeptide chain by a mechanism in which the hydroxyl group of a threonine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
A subcompartment of the endoplasmic reticulum consisting of tubules having membranes with high curvature in cross-section. [GOC:vw, PMID:16469703, PMID:20434336]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol. [ISBN:0198506732]
The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol. [CHEBI:28874, ISBN:0198506732]
Catalysis of the reaction: ATP + a phosphatidylinositol phosphate = ADP + a phosphatidylinositol bisphosphate. [EC:2.7.1.-, PMID:9759495]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
The lipid bilayer surrounding a cytoplasmic vesicle. [GOC:mah]
A vesicle that mediates transport between the trans-Golgi network and other parts of the cell. [GOC:mah]
A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes. [GOC:mah, PMID:11252894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes. [GOC:mah, ISBN:0198506732, NIF_Subcellular:sao1969557946, PMID:10559856, PMID:17284835]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
Any process that stops or reduces the activity of the enzyme lipoprotein lipase. [GOC:ai]
Transport of a vesicle from the plasma membrane to the endosome. [GOC:jid]
A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:ceb, GOC:jc, GOC:signaling, PMID:12065629, Wikipedia:Trk_receptor]
The directed movement of the hexose monosaccharide glucose into a cell or organelle. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation. [GOC:go_curators]
A series of molecular signals initiated by the binding of nerve growth factor (NGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, PMID:11520933, PR:000011194, Wikipedia:Nerve_growth_factor]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms. [GOC:mah, ISBN:0198506732]
The directed movement of substances from endosomes to lysosomes or vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the target compartment. [GOC:mah, PMID:12461556, PMID:16689637]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. [GOC:mah]
The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. [GOC:mtg_muscle]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered. [GOC:mah, GOC:mtg_apoptosis]
The directed movement of substances from endosomes to lysosomes. [GOC:ai, ISBN:0716731363]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. [GOC:mah, ISBN:0198506732, ISBN:0716731363]
The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes. [GOC:jl, ISBN:0716731363, PMID:10873832]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with nerve growth factor (NGF). [GOC:dgh]
Combining with neurotensin, a neuropeptide active in the central and peripheral nervous system in mammals, and transmitting the signal from one side of the membrane to the other by a mechanism independent of coupling to G proteins. [GOC:mah, GOC:signaling, PMID:9756851]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Combining with nerve growth factor (NGF), to prevent apoptosis in neurons and promote nerve growth, or to initiate a change in cell activity. [GOC:dph, GOC:tb]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. [GOC:txnOH]
A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome. [PMID:11019806, PMID:12186635, PMID:14570571]
A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane. [PMID:10099709, PMID:12563290]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. [GOC:hjd, PMID:10572093, PMID:12154376, PMID:16773132, PMID:18617898]
Any process that modulates the frequency, rate or extent of the IRE1-mediated unfolded protein response. [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22013210]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of signal transduction mediated by the JNK cascade. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The removal of one or more ubiquitin groups from a protein. [GOC:ai]
The removal of a ubiquitin-like protein of the NEDD8 type from a protein. [GOC:krc]
Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein. [GOC:jh2, ISBN:0120793709]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules. [GOC:elh]
Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. [GOC:ai, GOC:dos, GOC:dph, GOC:tb]
A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage. [GOC:mtg_cell_cycle]
The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. [GOC:ai, GOC:jl]
Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue. [ISBN:0198506732]
The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. [GOC:as, ISBN:0198506732]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. [EC:3.1.4, GOC:curators]
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. [PMID:16645198, PMID:20044567]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis, GOC:yaf, PMID:17340152]
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of membrane protein ectodomain peptidolysis. [GOC:ai]
Any process that decreases the stability of an RNA molecule, making it more vulnerable to degradative processes. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. [GOC:ai]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling]
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:add, ISBN:0721601464]
A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered. [GOC:go_curators, GOC:mtg_apoptosis]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function. [GOC:jl, http://lookwayup.com/]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. [GOC:ai, GOC:dgf]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35. [GOC:bf, PMID:26220253, PMID:27385586, PMID:9700157]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport. [GOC:jl, PMID:10873832, PMID:16936697]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The chemical reactions and pathways by which arachidonic acid is converted to other compounds including epoxyeicosatrienoic acids and dihydroxyeicosatrienoic acids. [GOC:mah, PMID:17979511]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [CHEBI:30413, GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. [GOC:mah]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of an NADPH- and oxygen-dependent reaction that converts arachidonic acid to a cis-epoxyeicosatrienoic acid. [http://lipidlibrary.aocs.org/Lipids/eic_hete/index.htm, PMID:10681399]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water. [http://www.onelook.com/, ISBN:0198506732]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA. [GOC:mcc, ISBN:0716730510]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His). [EC:6.1.1.21]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. [ISBN:0815316194]
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. [GOC:ef, GOC:mtg_muscle, ISBN:0198506732]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process in which a relatively unspecialized cell acquires specialized features of the embryonic placenta. [GOC:dph]
The process whose specific outcome is the progression of the parathyroid gland over time, from its formation to the mature structure. The parathyroid gland is an organ specialised for secretion of parathyroid hormone. [GOC:dph, ISBN:0721662544]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia. [GOC:dgh, GOC:jid]
Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell. [GOC:mah]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. [GOC:ceb, GOC:mah]
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter. [GOC:txnOH]
The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate. [GOC:ai]
Catalysis of the hydrolysis of any O-glycosyl bond. [GOC:mah]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A transmembrane heterodimeric protein located in the membrane of the rough endoplasmic reticulum. Both subunits contain GTPase domains with which signal recognition particle interacts. In the presence of GTP and SRP receptor, SRP is released from the ribosome-nascent chain complex. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory. [http://www.onelook.com/, ISBN:0721619908]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The side (leaflet) of the early endosome membrane that faces the cytoplasm. [GOC:lr]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. [GOC:go_curators, ISBN:0198506732]
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. [PMID:16645198, PMID:20044567]
Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it. [GOC:dph, GOC:mc, GOC:nln, PMID:10218156, PMID:8409967]
A prolongation or process extending from a cell, e.g. a flagellum or axon. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. [GOC:jl, PMID:11584301]
The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon. [GOC:pad, GOC:PARL]
The lipid bilayer surrounding an early endosome. [GOC:pz]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
The lipid bilayer surrounding a phagocytic vesicle. [GOC:mah]
A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting. [GOC:go_curators, PMID:19696797]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. [GOC:jl, ISBN:0395825172, ISBN:0815316194]
The lipid bilayer surrounding an endosome. [GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. [GOC:mah, GOC:tb]
A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork. [ISBN:0124325653]
Any process that modulates the frequency, rate or extent of synaptic vesicle exocytosis. [GOC:obol]
A receptor internalization process that contributes to canonical Wnt signaling pathway. [GOC:BHF, GOC:mah, PMID:16890161]
Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone. [GOC:ai, GOC:dph, GOC:tb]
Any process that modulates the volume of an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of exocytosis. [GOC:go_curators]
The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs. [ISBN:0815316194]
The replication of a viral RNA genome. [GOC:bf, GOC:jl]
The trafficking of synaptic vesicles from the pre-synaptic membrane so the vesicle can dock and prime for another round of exocytosis and neurotransmitter release. Recycling occurs after synaptic vesicle exocytosis, and is necessary to replenish presynaptic vesicle pools, sustain transmitter release and preserve the structural integrity of the presynaptic membrane. Recycling can occur following transient fusion with the presynaptic membrane (kiss and run), or via endocytosis of presynaptic membrane. [GOC:bf, GOC:pad, GOC:PARL, PMID:15217342, PMID:22026965, PMID:23245563]
Any process that modulates the frequency, rate or extent of endocytosis. [GOC:go_curators]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. [ISBN:0198506732]
A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. [GOC:mah, ISBN:0198506732, ISBN:0716731363]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate. [GOC:ai]
Interacting selectively and non-covalently with guanyl nucleotides, any compound consisting of guanosine esterified with (ortho)phosphate. [ISBN:0198506732]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells. The keratins are the most diverse classes of IF proteins, with a large number of keratin isoforms being expressed. Each type of epithelium always expresses a characteristic combination of type I and type II keratins. [ISBN:0716731363]
A spliceosomal complex that is formed following the release of the spliced product from the post-spliceosomal complex and contains the excised intron and the U2, U5 and U6 snRNPs. [GOC:ab, GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393, PMID:19239890]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site. [GOC:krc, GOC:mah, PMID:11574683, PMID:11971955]
Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA. [GOC:editors, GOC:mah, ISBN:0198547684, PMID:19239890]
The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced. [GOC:krc, ISBN:0198506732, ISBN:0879695897]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix. [GOC:mah, ISBN:0198506732]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with double-stranded RNA. [GOC:jl]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A transmembrane protein complex that is involved in protein folding in the endoplasmic reticulum. In S. cerevisiae, it has six members: EMC1, EMC2, AIM27, EMC4, KRE27, and EMC6. [GOC:dgf, PMID:19325107]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A protein folding process that takes place in the endoplasmic reticulum (ER). Secreted, plasma membrane and organelle proteins are folded in the ER, assisted by chaperones and foldases (protein disulphide isomerases), and additional factors required for optimal folding (ATP, Ca2+ and an oxidizing environment to allow disulfide bond formation). [GOC:mah, GOC:vw]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures. [PMID:10754561]
Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. [GOC:jl]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. [GOC:txnOH]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. [GOC:txnOH]
Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. [GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:krc]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:jl, GOC:txnOH, SO:0005836]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. [GOC:mtg_mpo, PMID:17572649]
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. [CL:0000062, GO_REF:0000034, GOC:jid]
The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate. [GOC:dph]
The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone. [GOC:dph]
The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract. [GOC:mtg_heart]
The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries. [GOC:mtg_heart, UBERON:0004145]
A transition where a cardiac epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell that will contribute to the formation of the endocardial cushion. [GOC:mtg_heart]
The increase in size or mass of an endochondral bone that contributes to the shaping of the bone. [GOC:ascb_2009, GOC:dph, GOC:tb]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. [GOC:mtg_signal]
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping. [GOC:bf, GOC:jl, ISBN:0395825172]
A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:signaling, ISBN:0878932437, PR:000000034]
Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor CREB. [GOC:dph, GOC:ecd, GOC:tb]
The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human. [ISBN:0198612001]
The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal. [ISBN:0198612001]
The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis. [GOC:bf, PMID:15269788]
The process, occurring in the embryo, by which the anatomical structures of a nail plate are generated and organized. The nail plate is the hard and translucent portion of the nail, composed of keratin, and serves to protect the tips of digits. [GOC:BHF, GOC:vk, ISBN:0323025781, PMID:11369996, UBERON:0008198, Wikipedia:Nail_(anatomy)]
The series of events that restore integrity to a damaged tissue, following an injury. [GOC:bf, PMID:15269788]
The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. [GOC:jl, GOC:mah]
The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe. [GOC:bf, GOC:jl, UBERON:0002544]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of keratinocyte differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of osteoblast differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. [CL:0000034, GOC:isa_complete]
The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. [DOI:10.1371/journal.pone.0051070, GOC:cjm, http://www.onelook.com]
Any process that activates or increases the frequency, rate or extent of catagen, the regression phase of the hair cycle. [GOC:ai]
The process of creating a trabecula in the bone. A trabecula is a tissue element in the form of a small beam, strut or rod. [GOC:dph]
The process in which bones are generated and organized. [GOC:dph]
The process in which the frontal suture is generated and organized. [GOC:dph, GOC:sl]
The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. [GOC:dph]
The process whose specific outcome is the progression of the mammary gland epithelium over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. [GOC:dph, GOC:yaf]
A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the progression of the heart over time. [GOC:dph, GOC:mtg_heart]
The process in which calcium salts, mainly carbonated hydroxyapatite, are deposited in tooth enamel. [GOC:BHF, GOC:mah, GOC:sl, PMID:10206335, PMID:16931858, PMID:21196346]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen. [GOC:mah]
Any process that starts the inactive process of meiosis. [GOC:dph, GOC:tb]
Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process. [GOC:mtg_apoptosis, GOC:obol]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
A complex of protein and RNA which facilitates translocation of proteins across membranes. [GOC:mlg]
A ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. Examples of this component are found in Mus musculus, Saccharomyces cerevisiae and Arabidopsis thaliana. [GOC:mtg_sensu, ISBN:0198506732]
The process in which SRP binds to the signal peptide in a nascent protein, causing protein elongation to pause, during cotranslational membrane targeting. [ISBN:0815316194]
The process during cotranslational membrane targeting wherein proteins move across a membrane. SRP and its receptor initiate the transfer of the nascent chain across the endoplasmic reticulum (ER) membrane; they then dissociate from the chain, which is transferred to a set of transmembrane proteins, collectively called the translocon. Once the nascent chain translocon complex is assembled, the elongating chain passes directly from the large ribosomal subunit into the centers of the translocon, a protein-lined channel within the membrane. The growing chain is never exposed to the cytosol and does not fold until it reaches the ER lumen. [ISBN:0716731363]
The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane. [ISBN:0716731363]
Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP). [GOC:jl, PMID:6181418]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL, TNF-related apoptosis inducing ligand. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. [GOC:jl, PMID:10891884]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling]
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:add, ISBN:0721601464]
Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues. [ISBN:0878932437]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
Interacting selectively and non-covalently with nerve growth factor (NGF). [GOC:dgh]
Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function. [GOC:jl, http://lookwayup.com/]
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. [GOC:go_curators, Wikipedia:Transmembrane_receptor]
A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1). [PMID:15571813, PMID:15688063]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:go_curators]
The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night). [GOC:jl]
Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours. [GOC:dph, GOC:jl, GOC:tb]
Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation. [GOC:mah]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by an SCF (Skp1/Cul1/F-box protein) complex, and mediated by the proteasome. [PMID:15380083]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. [GOC:BioGRID, GOC:jh2, PMID:9635407]
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells. [GOC:hb, GOC:mah, GOC:pr]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes. [GOC:mah, ISBN:0815332181]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The small subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis. [GOC:jl]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. [GOC:curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
The lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
Any process that maintains the redox environment of a cell or compartment within a cell. [GOC:ai, GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen. [GOC:cjm, GOC:mah]
The oxidation of peptidyl-cysteine to peptidyl-L-cysteine sulfinic acid or peptidyl-L-cysteine sulfenic acid. [PMID:9586994, RESID:AA0205, RESID:AA0262]
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GOC:go_curators, GOC:rb]
Catalysis of the reaction: 4 R'C(R)SH + O2 = 2 R'C(R)S-S(R)CR' + 2 H2O. [EC:1.8.3.2]
Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins. [EC:5.3.4.1, GOC:vw, http://en.wikipedia.org/wiki/Protein_disulfide-isomerase#Function]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein. [GOC:mah]
The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide. [GOC:elh, GOC:vw, PMID:10535901]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. [GOC:hb]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
Interacting selectively and non-covalently and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers. [GOC:mah, PMID:15556404, PMID:17525341]
Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation. [GOC:ecd]
Interacting selectively and non-covalently with a polymer of ubiqutin. [GOC:mah]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GOC:go_curators]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of receptor recycling. [GOC:add]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels. [GOC:bf, ISBN:0198506732]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins. [GOC:go_curators, Pfam:PF00595]
Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse. [ISBN:0198506732]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
Interacting selectively and non-covalently with the SNAP receptor syntaxin-1. [GOC:ai]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process in which a relatively unspecialized cell acquires specialized features of a bipolar cell, the last neuron to be generated in the retina. [GOC:ascb_2009, GOC:bf, GOC:dph, GOC:tb]
The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. [GOC:dph]
A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state. [GOC:dph, GOC:jl]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:jl, GOC:txnOH, SO:0005836]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
A vesicle-mediated transport process in which transmembrane proteins are ubiquitylated to facilitate their entry into luminal vesicles of multivesicular bodies (MVBs); upon subsequent fusion of MVBs with lysosomes or vacuoles, the cargo proteins are degraded. [GOC:mah, PMID:17603537]
Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of exocytosis. [GOC:go_curators]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
The process whose specific outcome is the progression of a keratinocyte over time, from its formation to the mature structure. [GOC:dph]
Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus. [GOC:mah]
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an erythropoietin stimulus. [GOC:yaf, PR:000007141]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-3 stimulus. [GOC:yaf, PR:000001387]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GOC:sl]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease. [GOC:jl, ISBN:0198506732]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity. [GOC:mah]
Any process that initiates the activity of an inactive protein kinase. [GOC:mah]
A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate. [GOC:mtg_signal, GOC:signaling]
The directed movement of a protein from the nucleus into the cytoplasm. [GOC:jl]
Binds to and increases the activity of a protein serine/threonine kinase. [GOC:go_curators]
Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group. [GOC:jl]
Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [EC:2.7.11.13, GOC:bf, GOC:mah]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A protein complex that possesses histone deacetylase activity. [GOC:mah]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. [GOC:jl]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. [GOC:bf, GOC:dph, ISBN:0815340729]
Any process pertaining to the functions of the nervous and muscular systems of an organism. [GOC:ai]
The chemical reactions and pathways involving neurotransmitters, any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. [CHEBI:25512, GOC:jl]
The removal of a glutamate residue from the side chain of a protein. Glutamate side chains are added to glutamic acid residues within the primary protein sequence during polyglutamylation. [GOC:sp, PMID:21074048]
The removal of a C-terminal, gene-encoded glutamate residue from a protein. [GOC:sp, PMID:21074048]
The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar Purkinje cell. Differentiation includes the processes involved in commitment of a neuroblast to a Purkinje cell fate. A Purkinje cell is an inhibitory GABAergic neuron found in the cerebellar cortex that projects to the deep cerebellar nuclei and brain stem. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15157725]
The process whose specific outcome is the progression of the cerebellar Purkinje cell layer over time, from its formation to the mature structure. The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg. [GOC:jid, GOC:pr, ISBN:0198606907]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms. [GOC:go_curators]
Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules. [GOC:clt]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [http://merops.sanger.ac.uk/about/glossary.htm#CARBOXYPEPTIDASE, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0198506732]
The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. [CL:0000062, GO_REF:0000034, GOC:jid]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The directed movement of hydrogen ion (proton) across a membrane. [GO_REF:0000069, GOC:pr, GOC:TermGenie]
The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase) in the mitochondrial inner membrane. [GOC:mah]
The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [GOC:go_curators, ISBN:0198506732]
The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis. [ISBN:0198506732, ISBN:0471331309]
Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O. [EC:1.9.3.1]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. [http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm, ISBN:0198506732]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure. [GOC:add, ISBN:0781735149]
Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation. [GOC:go_curators]
A two-stranded helical polymer of the protein actin. [GOC:mah]
The portion of the plasma membrane surrounding a cell surface projection. [GOC:mah]
The migrating motile tip of a growing nerve cell axon or dendrite. [ISBN:0815316194]
Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. [GOC:mah, GOC:pr, ISBN:0815316194]
A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments. [ISBN:0815316194]
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. [ISBN:0813516194]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork. [ISBN:0124325653]
The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. [GOC:ai]
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, http://en.wikipedia.org/wiki/Cell_migration]
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. [GOC:go_curators, ISBN:0521436125]
The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. [GOC:dph, GOC:go_curators]
Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. [GOC:mah]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. [GOC:bf, GOC:mah, GOC:vw]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
Any process in which the symbiont activates, maintains or increases its size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction. [GOC:jl, GOC:pamgo_curators]
The directed movement of sterols into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. [GOC:ai]
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [ISBN:0198506732]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position. [GOC:bf, GOC:mah]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
Enables the directed movement of sterols into, out of or within a cell, or between cells. Sterol are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. [GOC:ai]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. [GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. [GOC:ai]
Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds. [GOC:jl]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP. [GOC:dph, GOC:mah, GOC:tb]
Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction. [GOC:go_curators]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the rate, frequency, or extent of the appearance of any platelet-derived growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:BHF]
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:add, ISBN:0121245462, ISBN:0896039986]
Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation. [CL:0000192, GOC:ebc]
The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis). [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343, ISBN:0878937420]
Any process that modulates the frequency, rate, or extent of production of vascular endothelial growth factor. [GOC:rl]
Any process that stops, prevents, or reduces the rate of production of a cytokine. [GOC:add, ISBN:0781735149]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that increases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of glia cell differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of neuron differentiation. [GOC:go_curators]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules. [GOC:add, GOC:jl, ISBN:0120781859, ISBN:0781735149]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:15771591, PMID:15928678]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules. [GOC:add, ISBN:0781735149, PMID:15224092, PMID:15771591]
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Interacting selectively and non-covalently with an antigen peptide. [GOC:add, GOC:jl, GOC:rv]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region. [GOC:dos, GOC:jl, GOC:mah]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. [GOC:mah]
A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. [GOC:mah, ISBN:0198506732, ISBN:0716731363]
Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives. [GOC:bf, ISBN:0198506732, PMID:11395417]
A spliceosomal snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. [GOC:pr, ISBN:0879695897, PMID:9452384]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
A ribonucleoprotein complex that contains small nuclear RNA U6. [GOC:krc, GOC:mah]
A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing. [GOC:clt, PMID:12730603]
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body. [GOC:mah, PMID:17429074]
Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. [GOC:mah]
The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells. [GOC:krc]
The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced. [GOC:krc, ISBN:0198506732, ISBN:0879695897]
The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome. [GOC:krc, GOC:mah, ISBN:0879695897]
The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions. [PMID:9476892]
Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 snRNA). [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
The action of a molecule that contributes to the structural integrity of the lens of an eye. [GOC:mah]
A large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues. [GOC:jl, GOC:rl, http://biotech.icmb.utexas.edu/search/dict-search.html, PMID:10580165]
A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:pde, GOC:rl]
A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that activates or increases the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [GOC:go_curators]
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [ISBN:0198506732]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
Binds to and increases the activity of an enzyme. [GOC:dph, GOC:mah, GOC:tb]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of cell adhesion. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat1 protein. [GOC:jl, PMID:10918594]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling]
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:add, ISBN:0721601464]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
Any process that activates or increases the frequency, rate, or extent of leukocyte migration. [GOC:add]
Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function. [GOC:jl, http://lookwayup.com/]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. [GOC:add, GOC:jl, ISBN:0120781859, PMID:15928678]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:15771591, PMID:15928678]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex. [GOC:add, ISBN:0781735149, PMID:15531770, PMID:15771591, PMID:16153240]
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient. [GOC:ecd, GOC:mah, ISBN:0198547684]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The directed movement of hydrogen ion (proton) across a membrane. [GO_REF:0000069, GOC:pr, GOC:TermGenie]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
Catalysis of an oxidation-reduction (redox) reaction in which a diphenol or related substance acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. [GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: CoQH2 + 2 ferricytochrome c = CoQ + 2 ferrocytochrome c + 2 H+. [EC:1.10.2.2, ISBN:0198547684]
A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone. [GOC:mtg_sensu, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein. [GOC:als, PMID:22853951, PMID:23175390]
The hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 26 in histone H3. [GOC:als, PMID:22853951]
The process by which an organism or tissue maintains a population of stem cells of a single type.  This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types. [GOC:mah, ISBN:0878932437]
The hydrolysis of peptidyl-arginine to form peptidyl-citrulline. [PMID:23175390, RESID:AA0214]
Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. [GOC:jid, GOC:vw, PMID:12697820]
The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA. [GOC:mah]
Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. [GOC:mah, GOC:vw, PMID:20404130]
Catalysis of the reaction: L-arginine + H2O = L-citrulline + NH3. [EC:3.5.3.6]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3. [EC:3.5.3.15]
Any process that increases cell size. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:dph, GOC:go_curators, GOC:tb]
Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it. [GOC:dph, GOC:jl]
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. [GOC:go_curators]
A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. [GOC:ai, GOC:dph]
The vesicular release of classical neurotransmitter molecules from a neuron, across a chemical synapse, the subsequent activation of neurotransmitter receptors of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. [GOC:jl, MeSH:D009435]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
Interacting selectively and non-covalently with an opioid receptor. [GOC:nln]
The action characteristic of a neuropeptide hormone, any peptide hormone that acts in the central nervous system. A neuropeptide is any of several types of molecules found in brain tissue, composed of short chains of amino acids; they include endorphins, enkephalins, vasopressin, and others. They are often localized in axon terminals at synapses and are classified as putative neurotransmitters, although some are also hormones. [GOC:mah]
Naturally occurring peptide that is an opioid (any non-alkaloid having an opiate-like effect that can be reversed by naloxone or other recognized morphine antagonist). These include Leu- and Met-enkephalin, dynorphin and neoendorphin, alpha, beta, gamma and delta endorphins formed from beta-lipotropin, various pronase-resistant peptides such as beta casamorphin, and other peptides whose opiate-like action seems to be indirect. [ISBN:0198506732]
A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:pde, GOC:rl]
A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell. [GOC:BHF, GOC:mah]
Any process that increases the rate, frequency or extent of sequestering of triglyceride. Triglyceride sequestration is the process of binding or confining any triester of glycerol such that it is separated from other components of a biological system. [GOC:BHF, GOC:dph, GOC:tb]
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [ISBN:0198506732]
Enables the directed movement of lipids into, out of or within a cell, or between cells. [GOC:ai]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The lipid bilayer surrounding a peroxisome. [GOC:mah]
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. [GOC:dph, GOC:tb]
The chemical reactions and pathways involving lipids, as carried out by individual cells. [GOC:jl]
The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier. [GOC:dgh, GOC:mah]
Formation of the junction between an axon and the glial cell that forms the myelin sheath. Paranodal junctions form at each paranode, i.e. at the ends of the unmyelinated nodes of Ranvier. [PMID:14715942]
The process in which the anatomical structure of the cerebellum is generated and organized. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. The cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The chemical reactions and pathways resulting in the formation of ether lipids, lipids that contain (normally) one lipid alcohol in ether linkage to one of the carbon atoms (normally C-1) of glycerol. [GOC:ma, ISBN:0198547684, PMID:15337120]
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GOC:go_curators, ISBN:0198547684]
The aggregation, arrangement and bonding together of a set of components to form a synapse.  This process ends when the synapse is mature (functional). [GOC:mah]
The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue. [ISBN:0198506732]
Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate. [EC:3.1.2.2]
Catalysis of the reaction: acyl-CoA + glycerone phosphate = 1-acylglycerone 3-phosphate + CoA. [EC:2.3.1.42, RHEA:17660]
Catalysis of the transfer of an acyl group to an oxygen atom on the acceptor molecule. [GOC:ai]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
A protein complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. The complex binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs and suppresses their translation by blocking the recruitment of the 43S ribosomal complex to m7G cap-bound eIF4G. In humans it includes RPL13A, EPRS, SYNCRIP and GAPDH; mouse complexes lack SYNCRIP. [GOC:br, PMID:15479637, PMID:23071094]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. [GOC:mah, GOC:pz]
A structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. [GOC:mah, GOC:tb]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far. [GOC:mah, PR:000000017]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. [GOC:jl]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of neutrophil extravasation. [GOC:BHF, GOC:mah]
A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis, PMID:15044679, PMID:20816705]
Any process that activates or increases the frequency, rate, or extent of production of monocyte chemotactic protein-1. [GOC:mah]
A series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:BHF, GOC:mah, GOC:signaling]
Any process that activates or increases the frequency, rate or extent of cell division. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. [GOC:ai]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of mitosis. [GOC:go_curators]
Any process that activates or increases angiogenesis. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2. [GOC:go_curators]
Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo. [PMID:12814944]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of interleukin-6 production. [GOC:mah]
A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling, PMID:19295629]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that increases or activates the frequency, rate, or extent of production of vascular endothelial growth factor. [GOC:BHF, GOC:rl]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
The series of events leading to growth of connective tissue when loss of tissues that are incapable of regeneration occurs, or when fibrinous exudate cannot be adequately cleared that contribute to an inflammatory response. [GOC:jal, ISBN:0721601871]
The heat generation process that results in a rise in body temperature above the normal, often as a response to infection. [GOC:dph, GOC:jl]
Interacting selectively and non-covalently with copper (Cu) ions. [GOC:ai]
Interacting selectively and non-covalently with the interleukin-1 receptor. [GOC:go_curators]
Functions to control the survival, growth, differentiation and effector function of tissues and cells. [ISBN:0198599471]
The component of the mitochondrial inner membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The protein transport machinery of the mitochondrial inner membrane that contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor. [EC:3.6.3.51, PMID:8851659]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The import of proteins across the outer and inner mitochondrial membranes into the matrix. Unfolded proteins enter the mitochondrial matrix with a chaperone protein; the information required to target the precursor protein from the cytosol to the mitochondrial matrix is contained within its N-terminal matrix-targeting sequence. Translocation of precursors to the matrix occurs at the rare sites where the outer and inner membranes are close together. [ISBN:0716731363]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated. [GOC:mtg_transport, ISBN:0815340729]
Enables the energy-independent facilitated diffusion, mediated by passage of proteins through a transmembrane aqueous pore or channel. [GOC:rb]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway. [GOC:dph, GOC:go_curators, GOC:tb]
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, http://en.wikipedia.org/wiki/Cell_migration]
The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state. [GOC:dph, GOC:go_curators, PMID:11532397]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M). [GOC:dph, GOC:mah, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol. [GOC:mah, ISBN:0815316194]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells. [GOC:mtg_cell_cycle]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
Interacting selectively and non-covalently with the beta subunit of the catenin complex. [GOC:bf]
The lipid bilayer surrounding a synaptic vesicle. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The directed movement of L-glutamate across a membrane. [PMID:21307582]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The directed movement of L-glutamate, the L enantiomer anion of 2-aminopentanedioic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai, GOC:dph, GOC:tb]
Enables the transfer of L-glutamate from one side of a membrane to the other. L-glutamate is the anion of 2-aminopentanedioic acid. [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Any of the heteromeric enzymes that act in the TCA cycle. [GOC:mah]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue. [GOC:isa_complete]
The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle. [ISBN:0198506732]
The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate. [ISBN:0198506732]
A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle. [ISBN:0198506732]
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. [EC:4.-.-.-, ISBN:0198547684]
Catalysis of the reaction: (S)-malate = fumarate + H(2)O. [EC:4.2.1.2, RHEA:12463]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules. [GOC:add, ISBN:0781735149, PMID:15224092, PMID:15771591]
Interacting selectively and non-covalently with an antigen peptide. [GOC:add, GOC:jl, GOC:rv]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
An adherens junction which connects a cell to another cell. [GOC:hb]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. [GOC:jl]
The attachment of one cell to another cell via adhesion molecules. [GOC:dos]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any cadherin binding that occurs as part of the process of cell-cell adhesion. [GOC:dos]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The core mediator complex has a stimulatory effect on basal transcription, and contains most of the same subdomains as the larger form of mediator complex -- a head domain comprising proteins known in Saccharomyces as Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; and a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p -- but lacks the regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan core mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins. [PMID:11454195, PMID:16168358, PMID:17870225]
A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins. [PMID:11454195, PMID:16168358, PMID:17870225]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any series of molecular signals generated as a consequence of an androgen binding to its receptor. [GOC:mah]
A series of molecular signals generated as a consequence of a intracellular steroid hormone receptor binding to one of its physiological ligands. [GOC:mah, GOC:signaling]
The process by which an organism or tissue maintains a population of stem cells of a single type.  This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types. [GOC:mah, ISBN:0878932437]
Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription. [GOC:mah, GOC:txnOH]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. [GOC:go_curators]
Any cell cycle regulatory process that decreases the rate or extent of progression of a cell from G2 to M phase of the mitotic cell cycle. [GOC:mtg_cell_cycle]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol. [CHEBI:28874, ISBN:0198506732]
The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The process whose specific outcome is the progression of the brain ventricular system over time, from its formation to the mature structure. The brain ventricular system consists of four communicating cavities within the brain that are continuous with the central canal of the spinal cord. These cavities include two lateral ventricles, the third ventricle and the fourth ventricle. Cerebrospinal fluid fills the ventricles and is produced by the choroid plexus. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
Catalysis of the transfer of acyl groups from an acyl-CoA to a lysophospholipid. [GOC:cjk]
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The removal of sugar residues from a glycosylated protein. [GOC:mah]
Catalysis of the endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn-structure. One N-acetyl-D-glucosamine residue remains attached to the protein; the rest of the oligosaccharide is released intact. [EC:3.2.1.96]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:dph, GOC:krc, PMID:12663868, PMID:14699511]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: bile acid(out) + Na+(out) = bile acid(in) + Na+(in). [TC:2.A.28.-.-]
A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. [GOC:bf, GOC:mah, PMID:9407099]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. [GOC:jl]
The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52). [GOC:bf, GOC:mg2, GOC:signaling, GOC:vs, PMID:11239468, PMID:15140882]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus. [GOC:sl]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-beta production. [GOC:mah]
Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. [GOC:bf, GOC:jl, PMID:12773372, Reactome:REACT_13696.1]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH]
Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. [GOC:txnOH]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. [GOC:dph, GOC:tb]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion. [GO_REF:0000058, GOC:pad, GOC:PARL, GOC:TermGenie, PMID:24270810]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:mah]
The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. [GOC:jl]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of N-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#AMINOPEPTIDASE, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds. [GOC:jl]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone. [GOC:mtg_sensu, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway. [GOC:dph, GOC:go_curators, GOC:tb]
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, http://en.wikipedia.org/wiki/Cell_migration]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M). [GOC:dph, GOC:mah, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol. [GOC:mah, ISBN:0815316194]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells. [GOC:mtg_cell_cycle]
Interacting selectively and non-covalently with the beta subunit of the catenin complex. [GOC:bf]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. [ISBN:0198506732]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome. [GOC:elh]
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
A process of chromosome organization that is involved in a meiotic cell cycle. [GOC:mah]
The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules. [GOC:elh, PMID:10357855]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. [PMID:12509526]
The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. [GOC:dph, GOC:go_curators]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. [GOC:ems, GOC:mtg_sensu]
A cell cycle process comprising the steps by which a cell progresses through male meiosis I, the first meiotic division in the male germline. [GOC:dph, GOC:mah]
The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity. [PMID:2087779]
The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Synapsis begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete. [GOC:mtg_cell_cycle, PMID:22582262, PMID:23117617]
The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles. [GOC:elh]
A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization. [GOC:devbiol, http://ovary.stanford.edu]
The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure. [GOC:go_curators]
The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA. [PMID:10357855]
Interacting selectively and non-covalently with single-stranded DNA. [GOC:elh, GOC:vw, PMID:22976174]
Interacting selectively and non-covalently with double-stranded DNA. [GOC:elh, GOC:vw]
Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. [GOC:krc, ISBN:0815332181, PMID:15563464]
Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA. [GOC:elh]
Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks. [GOC:mah, ISBN:0198547684]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
The lipid bilayer surrounding a cytoplasmic vesicle. [GOC:mah]
The coat found on coated pits and the coated vesicles derived from coated pits; comprises clathrin and the AP-2 adaptor complex. [GOC:mah]
A clathrin coat found on a vesicle of the trans-Golgi network. [GOC:mah]
Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules. [GOC:mah]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes. [GOC:mah, ISBN:0198506732, NIF_Subcellular:sao1969557946, PMID:10559856, PMID:17284835]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. [GOC:ai, GOC:mah, ISBN:08789310662000]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle. [ISBN:0198547684]
A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. [GOC:bf, GOC:dph, ISBN:0815340729]
Any process that stops, prevents, or reduces the frequency, rate or extent of centriole replication. [GOC:ai]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
The lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
The chemical reactions and pathways resulting in the formation of chondroitin sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. [GOC:ai]
The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:mah, ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. [GOC:mah, ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans. [GOC:mah, ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues. [GOC:mah, ISBN:0198506732, ISBN:0198547684, RESID:AA0210]
The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. [ISBN:0192800981]
Catalysis of the transfer of a beta-D-xylosyl residue from UDP-D-xylose to the serine hydroxyl group of an acceptor protein substrate. [EC:2.4.2.26]
Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of an N-acetylglucosaminyl residue from UDP-N-acetyl-glucosamine to a sugar. [ISBN:0198506732]
A heterohexameric protein complex that is involved in modification of wobble nucleosides in tRNA. The complex can associate physically with hyperphosphorylated RNA polymerase II; it contains two discrete heterotrimeric subcomplexes. [GOC:bhm, GOC:jh, GOC:mah, GOC:vw, PMID:11435442, PMID:11689709, PMID:15769872, PMID:17018299, PMID:18755837, PMID:23165209]
Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation. [GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A protein complex that possesses histone acetyltransferase activity. [GOC:mah]
Any process that modulates the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
The modification of histone H4 by the addition of an acetyl group. [GOC:jl]
The modification of histone H3 by the addition of an acetyl group. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of cell migration. [GOC:go_curators]
The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. [GOC:bf, GOC:jid, ISBN:0582227089]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature. [CL:0000540, GOC:go_curators]
Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms. [GOC:ai]
Catalysis of the reaction: acetyl-CoA + histone H4 = CoA + acetyl-histone H4. [EC:2.3.1.48]
Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3. [EC:2.3.1.48]
Modulation of the activity of the enzyme phosphorylase kinase. [EC:2.7.11.19]
Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule. [GOC:ai]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits. [GOC:txnOH]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
Any process that modulates the frequency, rate or extent of initiation of DNA-dependent DNA replication; the process in which DNA becomes competent to replicate. In eukaryotes, replication competence is established in early G1 and lost during the ensuing S phase. [GOC:mah]
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. [GOC:mah]
Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template. [PMID:10357855]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines. [GOC:mtg_muscle, ISBN:0198506732, ISBN:0815316194]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, ISBN:0815316194]
A filament of myosin found in a muscle cell of any type. [GOC:mah]
The aggregation, arrangement and bonding together of proteins to form the myosin-based thick filaments of myofibrils in striated muscle. [GOC:mah]
The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. [GOC:bf]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. [GOC:mah]
A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope. [GOC:jl, GOC:mtg_muscle, ISBN:0198506732]
The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell, providing elasticity and recoiling. [GOC:BHF, GOC:rl, PMID:23283722]
Interacting selectively and non-covalently with muscle isoforms of actinin. Muscle alpha-actinin isoforms are found in skeletal and cardiac muscle and are localized to the Z-disc. [PMID:10984498, PMID:11699871, PMID:15014165]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
The action of a molecule that contributes to the structural integrity of a muscle fiber. [GOC:mah]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. [GOC:mah]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice. [GOC:cab2]
The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. [ISBN:0198547684]
The covalent attachment of a hydroxyl group to one or more fatty acids in a lipid. [GOC:hjd, PMID:15658937]
Catalysis of the reaction: estrogen + donor-H2 + O2 = 16-alpha-hydroxyestrogen + H2O. [GOC:BHF]
Catalysis of the hydroxylation of C-24 of any form of vitamin D. [GOC:BHF, GOC:mah, PMID:15546903]
Catalysis of the reduction of an aliphatic ring to yield an aromatic ring. [GOC:cb]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [CHEBI:30413, GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor. [GOC:mah]
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. [GOC:mah]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water. [http://www.onelook.com/, ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. [ISBN:0879693568]
A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components.  Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. [GOC:cjm, ISBN:0815316194]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP). [GOC:mah, ISBN:0815316194]
Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate. [GOC:mah, GOC:vw, ISBN:0815316194, PMID:11242086]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work. [GOC:mah, http://www.proweb.org/kinesin//KinesinMotility.html, http://www.proweb.org/kinesin//KinesinStructure.html]
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction. [EC:3.6.1.3, GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane. [GOC:jl, ISBN:0815316194]
A protein complex that contains two G-protein coupled receptors (GPCRs) of the same subtype. Formation of a GPCR homodimer may be important for the transport of newly formed receptors to the cell surface, and the function of the receptor. [GOC:al, GOC:bf, PMID:10713101, PMID:16670762]
A protein complex that contains two G-protein coupled receptors. [GOC:al, GOC:bf, PMID:10713101]
A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. [GOC:mah]
Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. [GOC:ai]
Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. [GOC:ai]
Any process that increases the concentration of calcium ions in the cytosol that occurs as part of a PLC-activating G-protein coupled receptor signaling pathway. G-protein-activated PLC hydrolyses phosphatidylinositol-bisphosphate (PIP2) to release diacylglycerol (DAG) and inositol trisphosphate (IP3). IP3 then binds to calcium release channels in the endoplasmic reticulum (ER) to trigger calcium ion release into the cytosol. [GOC:ai, GOC:signaling]
Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade. [GOC:go_curators]
A series of molecular signals initiated by an extracellular signal combining with a dimeric receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Heterodimeric and homodimeric GPCRs may have different functional properties from those of the respective monomers. [GOC:al, GOC:bf, PMID:15979374, PMID:21063387]
The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process. [http://www.onelook.com/]
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GOC:dph]
A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling, PMID:9131252]
The series of molecular signals generated as a consequence of a G-protein coupled glutamate receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP). [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The initiation of the activity of the inactive enzyme MAP kinase (MAPK). [PMID:9561267]
The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK). [PMID:9561267]
Combining with glutamate and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:ai, GOC:signaling]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The directed movement of pyruvate across a membrane. [GOC:TermGenie]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The directed movement of lactate across a membrane by means of some agent such as a transporter or pore. Lactate is 2-hydroxypropanoate, CH3-CHOH-COOH; L(+)-lactate is formed by anaerobic glycolysis in animal tissues, and DL-lactate is found in sour milk, molasses and certain fruit juices. [GOC:mcc, ISBN:0198506732]
The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:krc]
Enables the transfer of pyruvate, 2-oxopropanoate, from one side of the membrane to the other. [GOC:ai]
Catalysis of the transfer of lactate from one side of the membrane to the other. Lactate is 2-hydroxypropanoate, CH3-CHOH-COOH; L(+)-lactate is formed by anaerobic glycolysis in animal tissues, and DL-lactate is found in sour milk, molasses and certain fruit juices. [GOC:ai, ISBN:0198506732]
Enables the transfer of monocarboxylic acids from one side of the membrane to the other. A monocarboxylic acid is an organic acid with one COOH group. [GOC:ai]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. [GOC:go_curators, Wikipedia:Transmembrane_receptor]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. [GOC:ai]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. [GOC:ai, GOC:bf]
The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. [GOC:ai, http://www.onelook.com/]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Combining with an odorant and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity in response to detection of smell. [GOC:bf, GOC:dph, GOC:sart, PMID:19135896, PMID:21041441]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue. [GOC:mah, ISBN:0185316194]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue. [ISBN:0198506732]
A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins. [PMID:11454195, PMID:16168358, PMID:17870225]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of RNA biosynthetic process. [GOC:dph]
Any process that activates or increases the frequency, rate or extent of hepatocyte proliferation. [GOC:BHF, GOC:mah]
Any process that activates or increases the frequency, rate or extent of receptor activity. [GOC:obol]
A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus. [GOC:sjw, PMID:9916872]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus. [GOC:mah]
Any process that modulates the frequency, rate or extent of vitamin D receptor signaling pathway activity. [GOC:BHF, GOC:mah]
An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell. [GOC:add, GOC:signaling, ISBN:0121245462, ISBN:0896039986, PMID:20811974]
A cell cycle process that activates or increases the rate or extent of the transition from the G0 quiescent state to the G1 phase. [GOC:mah]
The multiplication or reproduction of mammary gland branch epithelial cells, resulting in the elongation of the branch. The mammary gland branch differs from the bud in that it is not the initial curved portion of the outgrowth. [GOC:dph]
The process in which the branching structure of the mammary gland duct is generated and organized as a part of pregnancy. [GOC:dph, PMID:19261859]
The process in which the branching structure of the mammary gland duct is generated and organized during the period of sexual maturity in mammals. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. [GOC:dph, PMID:19261859]
Any process that increases the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor. [GOC:dph]
The process aimed at the progression of an enucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. [GOC:devbiol]
The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure. [GOC:devbiol]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of keratinocyte differentiation. [GOC:go_curators]
The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. [CL:0000136, GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. [GOC:go_curators, GOC:mtg_sensu]
The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. [GOC:jl, ISBN:0321000382]
The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow. [CL:0000556, GOC:BHF, GOC:vk]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus. [GOC:bf]
The series of molecular signals initiated by binding of a ligand to any of the peroxisome proliferator activated receptors (alpha, beta or gamma) in the nuclear membrane, and ending with the initiation or termination of the transcription of target genes. [GOC:BHF, PMID:18221086]
The stages of blood cell formation that take place within the embryo. [GOC:bf]
The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal. [ISBN:0198612001]
The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field. [GOC:go_curators]
Any process that activates or increases the rate or extent of mammary gland epithelial cell proliferation. [GOC:mah]
The multiplication or reproduction of mammary gland epithelial cells, resulting in the expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. [GOC:dph, GOC:mah]
Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the activity of an intracellular estrogen receptor signaling pathway. [GOC:mah]
The regrowth of a lost or destroyed animal organ. [GOC:mah]
Any series of molecular signals generated as a consequence of an androgen binding to its receptor. [GOC:mah]
A series of molecular signals generated as a consequence of a intracellular steroid hormone receptor binding to one of its physiological ligands. [GOC:mah, GOC:signaling]
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. [GOC:mah]
The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte. [GOC:dph, GOC:mah, GOC:sdb_2009, GOC:tb]
Any process that decreases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population. [GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. [GOC:dgh, GOC:go_curators, ISBN:0471245208, ISBN:0721662544]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The secretion of milk by the mammary gland. [ISBN:0198506732]
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:jid, UBERON:0000948]
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). [GOC:dph, GOC:jid, GOC:tb, UBERON:0000955]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
The chemical reactions and pathways resulting in the formation of androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics. [ISBN:0198506732]
The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones. [GOC:jl, ISBN:0716720094]
Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription. [GOC:mah, GOC:txnOH]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells. [GOC:ascb_2009, GOC:dph, GOC:tb]
The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized. [GOC:mtg_heart]
A series of molecular signals mediated by the detection of a thyroid hormone. [GOC:hjd]
The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus. [GOC:dph, ISBN:0582064333]
The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin. [GOC:add, ISBN:068340007X]
The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes. [GOC:add, ISBN:068340007X]
The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. [GOC:go_curators, GOC:mtg_sensu]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
The developmental process in which the size or shape of a cell is generated and organized. [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with the LBD, the ligand binding domain found in nuclear receptors. In general, the LBDs consist of three layers comprised of twelve alpha-helices and several beta-strands that are organized around a lipophilic ligand-binding pocket. [PMID:9682036]
Interacting selectively and non-covalently with a thyroid hormone receptor. [GOC:ai]
Interacting selectively and non-covalently with any of the peroxisome proliferator activated receptors, alpha, beta or gamma. [GOC:jl, PMID:12769781]
Interacting selectively and non-covalently with the retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily. [GOC:jl, PMID:12476796]
Interacting selectively and non-covalently with the vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes. [GOC:jl, PMID:12637589]
Interacting selectively and non-covalently with a mediator complex. The mediator complex is a protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins. [GOC:yaf, PMID:18391015]
Interacting selectively and non-covalently with a nuclear hormone receptor, a ligand-dependent receptor found in the nucleus of the cell. [GOC:bf]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
The function of a transcription cofactor that activates transcription in conjunction with a thyroid hormone-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself. [GOC:dph, GOC:tb]
The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself. [GOC:dph, GOC:tb]
Interacting selectively and non-covalently with an estrogen receptor. [GOC:ai]
Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein. [GOC:mah, PMID:7776974]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH]
A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components.  Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. [GOC:cjm, ISBN:0815316194]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP). [GOC:mah, ISBN:0815316194]
Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate. [GOC:mah, GOC:vw, ISBN:0815316194, PMID:11242086]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The area in the center of the spindle where the spindle microtubules from opposite poles overlap. [GOC:ai, PMID:15296749]
A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis. [ISBN:0815316194]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. [ISBN:0879693568]
Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work. [GOC:mah, http://www.proweb.org/kinesin//KinesinMotility.html, http://www.proweb.org/kinesin//KinesinStructure.html]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle. [GOC:mtg_cell_cycle]
Any process that modulates the frequency, rate or extent of cell maturation. [GO_REF:0000058, GOC:TermGenie, PMID:17459944]
A process that is part of the mitotic cell cycle. [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie]
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. [GOC:di, GOC:go_curators, GOC:pr]
The directed movement of a protein to a specific location. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons. [GOC:go_curators, GOC:mtg_apoptosis]
Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons. [GOC:go_curators, GOC:mtg_apoptosis]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate. [GOC:mah, GOC:pf, PMID:17050732]
Any process that stops, prevents, or reduces the frequency, rate, or extent of integrin activation. [GOC:add]
Any process that modulates the frequency, rate or extent of Rap protein signal transduction. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells. [GOC:mah]
Any process that initiates the activity of an inactive protein kinase. [GOC:mah]
Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons. [GOC:mah]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by an SCF (Skp1/Cul1/F-box protein) complex, and mediated by the proteasome. [PMID:15380083]
Any process that modulates the frequency, rate or extent of cell migration. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. [GOC:mah]
The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The creation of greater cell numbers in the forebrain due to cell division of progenitor cells. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
The progression of the hippocampus over time from its initial formation until its mature state. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420, UBERON:0002421]
The process whose specific outcome is the progression of the cerebellar cortex over time, from its formation to the mature structure. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The process that contributes to the act of creating the structural organization of the cerebellar Purkinje cell layer. This process pertains to the physical shaping of a rudimentary structure. The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The process that contributes to the act of creating the structural organization of the cerebellar granule layer. This process pertains to the physical shaping of a rudimentary structure. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
Any process that modulates the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle. [GOC:mtg_cell_cycle, PMID:17329565]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis. [GOC:mah, ISBN:0815316194]
Any process that modulates the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins. [GOC:go_curators, Pfam:PF00595]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules. [GOC:clt]
Catalysis of movement along a microtubule toward the plus end, coupled to the hydrolysis of ATP. [EC:3.6.4.4, GOC:vw]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
A disulfide-bonded, heterotetrameric receptor complex. The alpha chains are entirely extracellular, while each beta chain has one transmembrane domain. The ligand binds to the alpha subunit extracellular domain and the kinase is associated with the beta subunit intracellular domain. [ISBN:0198506732]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The series of molecular signals generated as a consequence of the insulin receptor binding to insulin. [GOC:ceb]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. [GOC:mah]
Interacting selectively and non-covalently with the insulin receptor. [GOC:ai]
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes. [GOC:mah, ISBN:0815332181]
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. [GOC:dgh, GOC:hb, GOC:mah]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential. [GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A process in which a potassium ion is transported from one side of a membrane to the other. [GOC:mah]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer. [GOC:ai]
Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. [GOC:mah]
The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient. [GOC:BHF, GOC:jl]
Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
Enables the transmembrane transfer of a potassium ion by a delayed rectifying voltage-gated channel. A delayed rectifying current-voltage relation is one where channel activation kinetics are time-dependent, and inactivation is slow. [GOC:mah, PMID:11343411, PMID:2462513]
Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0815340729]
Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The chemical reactions and pathways involving L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine). [CHEBI:16946, GOC:yaf]
The chemical reactions and pathways involving kynurenine, the amino acid 3-(2-aminobenzoyl)-alanine. [CHEBI:28683, GOC:mah, GOC:rph]
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. [GOC:curators, ISBN:0198547684]
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells. [CHEBI:33709, GOC:curators, ISBN:0198506732]
The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism. [ISBN:0198506732]
Catalysis of the reaction: L-kynurenine + glyoxylate = 4-(2-aminophenyl)-2,4-dioxobutanoate + glycine. [EC:2.6.1.63, RHEA:19252]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. [GOC:mah, ISBN:0198506732]
Catalysis of the reaction: L-kynurenine + 2-oxoglutarate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-glutamate. [EC:2.6.1.7]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide. [GOC:dos, GOC:vw]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that maintains the redox environment of a cell or compartment within a cell. [GOC:ai, GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen radical stimulus. An oxygen radical is any oxygen species that carries a free electron; examples include hydroxyl radicals and the superoxide anion. [GOC:krc, ISBN:0124325653]
Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP. [GOC:jl]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: NADP(+) + thioredoxin = H(+) + NADPH + thioredoxin disulfide. [EC:1.8.1.9, RHEA:20348]
The small subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The directed movement of a protein to a specific location in the Golgi apparatus. [GOC:mah]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:pde, GOC:rl]
A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that stops or reduces the activity of the enzyme lipoprotein lipase. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids. [GOC:go_curators]
The chemical reactions and pathways involving any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids. [ISBN:0198506732]
The process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded. [GOC:BHF, GOC:rl]
The process in which a chylomicron remnant is removed from the blood via receptor-mediated endocytosis into liver cells and its constituent parts degraded. [GOC:BHF, GOC:mah, GOC:pde]
The acquisition, loss or modification of a protein or lipid within a plasma lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the esterification of cholesterol by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT). [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
The directed movement of a phospholipid out of a cell or organelle. [GOC:mah]
The directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle. [GOC:sart]
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of cholesterol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:mah]
Any process that decreases the rate, frequency or extent of very-low-density lipoprotein particle clearance. Very-low-density lipoprotein particle clearance is the process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded. [GOC:BHF, GOC:dph, GOC:tb]
Any process that decreases the rate, frequency or extent of phosphatidylcholine catabolism. Phosphatidylcholine catabolic processes are the chemical reactions and pathways resulting in the breakdown of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline. [GOC:BHF, GOC:tb]
The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. [ISBN:0198506732]
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [ISBN:0198506732]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins. [ISBN:0198506732]
Stops, prevents or reduces the activity of a lipase, an enzyme that catalyzes of the hydrolysis of a lipid. [GOC:BHF, GOC:rl]
Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. [ISBN:0198506732]
Stops, prevents or reduces the activity of a phospholipase, an enzyme that catalyzes of the hydrolysis of a phospholipid. [GOC:ai, GOC:rl]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
The lipid bilayer surrounding an early endosome. [GOC:pz]
Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives. [GOC:bf, ISBN:0198506732, PMID:11395417]
Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position. [GOC:bf, PMID:10209156, PMID:11395417, PMID:11557775]
Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions. [GOC:bf, GOC:jl]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. [GOC:jl]
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. [ISBN:0471245208]
The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open. [GOC:dph, UBERON:0002073]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. [GOC:dph, GOC:rl, GOC:tb]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Interacting selectively and non-covalently with the protein-tyrosine kinase receptor Neu/ErbB-2/HER2. [GOC:jl]
A cell-substrate junction (attachment structure) found in epithelial cells that links intermediate filaments to extracellular matrices via transmembrane complexes. In vertebrates, hemidesmosomes mediate contact between the basal side of epithelial cells and the basal lamina. In C. elegans, hemidesmosomes connect epithelial cells to distinct extracellular matrices on both the apical and basal cell surfaces. [GOC:kmv, ISBN:0815316208, PMID:20205195]
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis. [GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 2 (NOD2) pathway. [GOC:add]
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:add, ISBN:0721601464]
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan. [GOC:add]
A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, PR:000006933]
The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. [GOC:ma]
Interacting selectively and non-covalently with an integrin. [GOC:ceb]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. NMDA receptors are composed of assemblies of NR1 subunits (Figure 3) and NR2 subunits, which can be one of four separate gene products (NR2A-D). Expression of both subunits are required to form functional channels. The glutamate binding domain is formed at the junction of NR1 and NR2 subunits. NMDA receptors are permeable to calcium ions as well as being permeable to other ions. Thus NMDA receptor activation leads to a calcium influx into the post-synaptic cells, a signal thought to be crucial for the induction of NMDA-receptor dependent LTP and LTD. [http://www.bris.ac.uk/Depts/Synaptic/info/glutamate.html]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential. [GOC:dph, GOC:ef]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus. [GOC:go_curators]
A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription. [GOC:signaling, ISBN:0198506732]
A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:mah]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with glycine, aminoethanoic acid. [GOC:ai]
Enables the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts. [ISBN:0198506732]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands. [PMID:17543136]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GOC:dph, GOC:tb]
A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
Interacting selectively and non-covalently with a glycoprotein, a protein that contains covalently bound glycose (monosaccharide) residues. These also include proteoglycans. [GOC:hjd, ISBN:0198506732]
A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5. [GOC:bm, PMID:7828851]
A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins. [PMID:10589671, PMID:11743021, PMID:12865422]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway. [GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of cellular senescence. [GOC:BHF]
The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa. [GOC:BHF, GOC:mah, UBERON:0001343]
The self-renewing division of a germline stem cell in the male gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the male gametes. [GOC:jid]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity. [GOC:go_curators]
Any process involved in the controlled movement of a flagellated sperm cell. [GOC:cilia, GOC:jl, GOC:krc]
The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups. [GOC:mah, GOC:vw]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. [GOC:dph, GOC:go_curators]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
A cell cycle process comprising the steps by which a cell progresses through male meiosis I, the first meiotic division in the male germline. [GOC:dph, GOC:mah]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. [GOC:mah, GOC:vw, PMID:20404130]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives. [GOC:bf, ISBN:0198506732, PMID:11395417]
Interacting selectively and non-covalently with a histone protein in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. [GOC:bf, PMID:14585615]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any process that increases the frequency, rate or extent of adenylate cyclase (AC) activity that is an integral part of a G-protein coupled receptor signaling pathway. [GOC:dph, GOC:signaling, GOC:tb]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. [GOC:go_curators, Wikipedia:Transmembrane_receptor]
The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation. [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:9412464]
A protein complex that consists of three components, NLRP3 (NALP3), PYCARD and caspase-1. It is activated upon exposure to whole pathogens, as well as a number of structurally diverse pathogen- and danger-associated molecular patterns (PAMPs and DAMPs) and environmental irritants. Whole pathogens demonstrated to activate the NLRP3 inflammasome complex include the fungi Candida albicans and Saccharomyces cerevisiae, bacteria that produce pore-forming toxins, including Listeria monocytogenes and Staphylococcus aureus, and viruses such as Sendai virus, adenovirus, and influenza virus. [GOC:add, GOC:BHF, GOC:vp, PMID:20303873]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A caspase-1-dependent cell death subroutine that is associated with the generation of pyrogenic mediators such as IL-1beta and IL-18. [GOC:mtg_apoptosis, PMID:18846107, PMID:21760595]
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer. [GOC:ai]
Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism. [GOC:ai]
Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell. [GOC:ai]
The aggregation, arrangement and bonding together of a set of components to form a pore complex. A pore complex is a small opening in a membrane that allows the passage of liquids and/or gases. [GOC:jl, GOC:mah]
The aggregation, arrangement and bonding together of a set of components by an organism to form a pore complex in a membrane of another organism. [GOC:bf, GOC:fj, PMID:21549739]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus. [GOC:mah]
The rupture of cell membranes and the loss of cytoplasm. [UniProtKB-KW:KW-0204]
Interacting selectively and non-covalently with cardiolipin. [GOC:kmv, GOC:TermGenie]
Interacting selectively and non-covalently with phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids. [CHEBI:16337, GOC:jp, ISBN:0198506732]
Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position. [GOC:bf, GOC:mah]
Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions. [GOC:bf, GOC:jl]
Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine. [ISBN:0198506732, PMID:12000961]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains about 10 polypeptide subunits including four redox centers: cytochrome b/b6, cytochrome c1 and an 2Fe-2S cluster. Catalyzes the oxidation of ubiquinol by oxidized cytochrome c1. [GOC:mtg_sensu, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The cleavage of peptide bonds in proteins, usually near the N terminus, contributing to the process of import into the mitochondrion. Several different peptidases mediate cleavage of proteins destined for different mitochondrial compartments. [GOC:mcc, PMID:12191769]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region. [GOC:dos, GOC:jl, GOC:mah]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments. [GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton). [GOC:mah]
The action of a molecule that contributes to the structural integrity of a cytoskeletal structure. [GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
Any process that modulates the rate, frequency, or extent of protein kinase A signaling. PKA signaling is the series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound. [GOC:BHF, GOC:dph, GOC:tb]
Interacting selectively and non-covalently with any subunit of protein kinase A. [GOC:ai]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core. [GOC:rb, http://en.wikipedia.org/wiki/Proteasome]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
The aggregation, arrangement and bonding together of a mature, active proteasome complex. [GOC:go_curators, PMID:10872471]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle. [GOC:mtg_cell_cycle, PMID:12360190]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus. [GOC:mah]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The chemical reactions and pathways involving urate, the anion of uric acid, 2,6,8-trioxypurine, the end product of purine metabolism in certain mammals and the main excretory product in uricotelic animals. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure. [PMID:9372908]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Interacting selectively and non-covalently with the tumor necrosis factor receptor. [GOC:ai]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that activates or increases the frequency, rate or extent of myoblast fusion. [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:21364645]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. [CL:0000056, GOC:go_curators, GOC:mtg_muscle]
Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation. [ISBN:0781735149]
Any process that increases the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus. [GOC:BHF, GOC:dph, GOC:tb]
The release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus. [GOC:jl]
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263]
Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis, PMID:14744432, Wikipedia:Caspase]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. [GOC:jl, ISBN:0198506732]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway. [GOC:mtg_apoptosis]
Any process that activates or increases the rate or extent of podosome assembly. [GOC:mah, GOC:sl]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. [GOC:mah]
A process in which a protein is transported to, or maintained in, a location within a tricellular tight junction. [PMID:24889144]
The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. [GOC:dph]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours. [GOC:dph, GOC:jl, GOC:tb]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions. [GOC:add, GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. [GOC:hb]
The process of introducing a phosphate group into a JUN protein. [GOC:jl]
An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell. [GOC:bf, GOC:signaling, PMID:11790549, PMID:20811974]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli. [GOC:ma, ISBN:0198547684]
Catalysis of the reaction: JUN + ATP = JUN phosphate + ADP. This reaction is the phosphorylation and activation of members of the JUN family, a gene family that encodes nuclear transcription factors. [GOC:bf, ISBN:0198506732]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. [GOC:ai]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. [GOC:ai, GOC:bf]
The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. [GOC:ai, http://www.onelook.com/]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell. [GOC:jl, ISBN:0721662544]
Combining with an odorant and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity in response to detection of smell. [GOC:bf, GOC:dph, GOC:sart, PMID:19135896, PMID:21041441]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone. [GOC:mtg_sensu, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein. [GOC:als, PMID:22853951, PMID:23175390]
The hydrolysis of peptidyl-arginine to form peptidyl-citrulline. [PMID:23175390, RESID:AA0214]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3. [EC:3.5.3.15]
The component of the autophagosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:autophagy, GOC:mf]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A type of secondary lysosome in which a primary lysosome has fused with the outer membrane of an autophagosome. It is involved in the second step of autophagy in which it degrades contents with acidic lysosomal hydrolases. [GOC:sart, NIF_Subcellular:sao8444068431, PMID:19008921]
The lipid bilayer surrounding a late endosome. [GOC:pz]
The lipid bilayer surrounding the platelet dense granule. [GOC:mah]
The lipid bilayer surrounding a phagocytic vesicle. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center. [NIF_Subcellular:nlx_subcell_20090702, PMID:11964142, PMID:2557062]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any cellular protein catabolic process that takes place in a lysosome. [GO_REF:0000062, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24334770]
The process in which autophagosomes, double-membraned vacuoles containing cytoplasmic material fuse with a vacuole (yeast) or lysosome (e.g. mammals and insects). In the case of yeast, inner membrane-bounded structures (autophagic bodies) appear in the vacuole. Fusion provides an acidic environment and digestive function to the interior of the autophagosome. [GOC:autophagy, GOC:lf, PMID:11099404, PMID:16874026, PMID:17534139]
The targeting of a protein to the lysosome process in which an input protein binds to a chaperone and subsequently to a lysosomal receptor. [GOC:dph, GOC:pad, GOC:PARL, PMID:22748206]
The autophagy process which begins when chaperones and co-chaperones recognize a KFERQ-related motif and unfold the substrate protein. The process ends with the catabolism of the protein in the lysosome. [GOC:pad, GOC:PARL, PMID:22743996]
Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation. [GOC:ai]
The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state. [GOC:mah, PMID:3091429, PMID:7781901]
Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation. [GOC:dph, GOC:mah, GOC:tb]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment. [GOC:jl]
The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation. [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:9412464]
The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. [GOC:ma]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. [GOC:elh, PMID:20404130]
The addition of an acetyl group to one or more amino acids in a protein, occurring after the protein has been completely translated and released from the ribosome. [GOC:mah]
The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other. [GOC:jh, GOC:mah, ISBN:0815316194]
Any process that modulates the frequency, rate or extent of DNA replication. [GOC:go_curators]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The small subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript. [GOC:curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A multisubunit protein complex that is involved in chromatin remodeling. It is required for the incorporation of the histone variant H2AZ into chromatin. In S. cerevisiae, the complex contains Swr1p, a Swi2/Snf2-related ATPase, and 12 additional subunits. [GOC:rb, PMID:14645854, PMID:14690608, PMID:19355820]
The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits. [GOC:jl, PMID:11735001, PMID:15066277]
Any process that modulates the frequency, rate or extent of the removal of acetyl groups from histones. [GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with the enzyme histone deacetylase. [GOC:jl]
Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. [GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles. [GOC:jl, GOC:mah, ISBN:0198506732]
The covalent attachment of a prenyl group to a protein; geranyl, farnesyl, or geranylgeranyl groups may be added. [GOC:di, ISBN:0198506732]
Catalysis of the covalent addition of an isoprenoid group such as a farnesyl or geranylgeranyl group via thioether linkages to a cysteine residue in a protein. [GOC:mah]
Conserved heterotrimeric complex of PCNA-like proteins that is loaded onto DNA at sites of DNA damage. [PMID:12531008]
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. [GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. [GOC:mah]
A mitotic cell cycle checkpoint that slows DNA synthesis in response to DNA damage by the prevention of new origin firing and the stabilization of slow replication fork progression. [GOC:vw]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds. [GOC:mtg_cell_cycle]
A cell cycle checkpoint that prevents the initiation of nuclear division until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome. [GOC:curators, GOC:rn, PMID:11728327, PMID:12537518]
A cell cycle process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction. [GOC:mtg_cell_cycle]
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. [GOC:ai]
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/]
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. [GOC:dgh, GOC:hb, GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. [ISBN:0879693568]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process. [GOC:BHF, GOC:mah, GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of establishment of cell polarity. [GOC:dph]
Any process that maintains the redox environment of a cell or compartment within a cell. [GOC:ai, GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of protein binding. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis. [GOC:go_curators]
Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium. [GOC:BHF, GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation. [GOC:add]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions. [GOC:bf, GOC:jl]
A protein complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. The complex binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs and suppresses their translation by blocking the recruitment of the 43S ribosomal complex to m7G cap-bound eIF4G. In humans it includes RPL13A, EPRS, SYNCRIP and GAPDH; mouse complexes lack SYNCRIP. [GOC:br, PMID:15479637, PMID:23071094]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The large subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). [ISBN:0198506732]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation preinitiation complex. [GOC:TermGenie]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far. [GOC:mah, PR:000000017]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers. [GOC:mah, PMID:11121744]
A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane. [PMID:10099709, PMID:12563290]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that stops, prevents or reduces the frequency, rate or extent of reactive oxygen species metabolic process. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of oxygen metabolic process. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of cysteine-type endopeptidase activity. [GOC:obol, GOC:yaf]
Any process that increases the frequency, rate or extent of the passage or uptake of molecules by the lysosomal membrane. [GOC:yaf, PMID:20544854]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus. [GOC:mah, GOC:yaf]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:mah]
An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell. [GOC:add, GOC:signaling, ISBN:0121245462, ISBN:0896039986, PMID:20811974]
Any process that decreases the rate, frequency or extent of necrotic cell death. Necrotic cell death is a cell death process that is morphologically characterized by a gain in cell volume (oncosis), swelling of organelles, plasma membrane rupture and subsequent loss of intracellular contents. [GOC:BHF, GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of protein glycosylation. Protein glycosylation is the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins. [GOC:dms, GOC:dph, GOC:pr]
Any process involved in the maintenance of an internal steady state of cadmium ions within an organism or cell. [GOC:ai, GOC:jid, GOC:mah]
Any process involved in the maintenance of an internal steady state of zinc ions within an organism or cell. [GOC:ai, GOC:jid, GOC:mah]
Any process that stops or reduces the rate of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. [GOC:ai]
Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the origin and formation of neurons. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells. [GOC:jl]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons. [GOC:go_curators, GOC:mtg_apoptosis]
A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound. [GOC:bf, PMID:20517722]
Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that activates or increases the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:rn, PMID:14978214, PMID:18439143]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GOC:sl]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:mah]
A series of molecular signals initiated by the binding of leptin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. [GOC:mah, GOC:signaling, GOC:yaf]
Any process that initiates the activity of the inactive enzyme protein kinase B. [GOC:pg]
Any process that modulates the frequency, rate or extent of a response to a food stimulus. [GOC:add]
Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity. [GOC:dgh]
Any process that stops, prevents, or reduces the frequency, rate or extent of axon outgrowth. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2). [CHEBI:18421, GOC:jl]
The covalent alteration of one or more amino acid residues within a histone protein. [GOC:krc]
The process aimed at the progression of an astrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function. [GOC:dgh, GOC:ef]
Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. [GOC:dph, GOC:tb]
Any process that increases the rate, frequency or extent of necrotic cell death. Necrotic cell death is a cell death process that is morphologically characterized by a gain in cell volume (oncosis), swelling of organelles, plasma membrane rupture and subsequent loss of intracellular contents. [PMID:16507998]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. [GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl, PMID:12115731]
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263]
Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell. [GOC:ai, GOC:mah]
Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell. [GOC:ai, GOC:mah]
The directed movement of zinc (Zn II) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. [GOC:ai]
The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:hjd]
A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope. [GOC:curators, ISBN:0198506732, PMID:14570049, PMID:9126736]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with cadmium (Cd) ions. [GOC:ai]
Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis, PMID:14744432, Wikipedia:Caspase]
Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with copper (Cu) ions. [GOC:ai]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. [EC:3.1.4, GOC:curators]
Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate. [EC:3.1.4.17]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:add, ISBN:0781735149]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The lipid bilayer surrounding a peroxisome. [GOC:mah]
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [GOC:go_curators]
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. [GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: 1-acyl-glycerone 3-phosphate + a long-chain alcohol = 1-alkyl-glycerone 3-phosphate + a long-chain acid anion. [EC:2.5.1.26]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The directed movement of glucose across a membrane. [GO_REF:0000069, GOC:TermGenie, PMID:9090050]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The directed movement of the hexose monosaccharide glucose into a cell or organelle. [GOC:ai]
The directed movement of hexose across a membrane by means of some agent such as a transporter or pore. Hexoses are any aldoses with a chain of six carbon atoms in the molecule. [GOC:vw]
The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:jl]
The directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other. [GOC:jid, GOC:mtg_transport, ISBN:0815340729]
Enables the transfer of a substance from one side of a membrane to the other. [GOC:mtg_transport, ISBN:0815340729]
Enables the transfer of the hexose monosaccharide glucose from one side of the membrane to the other. [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sugar(out) + H+(out) = sugar(in) + H+(in). [TC:2.A.1.1.-]
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. [GOC:ai, GOC:dgf]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. [GOC:go_curators, ISBN:0198506732]
Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters. [GOC:ai]
Catalysis of the hydrolysis of any ester bond. [GOC:jl]
Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. [GOC:mah, ISBN:0198547684]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell. [GOC:ai, GOC:mah]
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [GOC:go_curators]
A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. [http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm, ISBN:0198506732]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization. [GOC:BHF]
Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP. [GOC:dph, GOC:mah, GOC:tb]
The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities. [GOC:mah, PMID:7693735]
Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. [GOC:ai, GOC:pr]
Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical. [GOC:ai]
Any process that activates, maintains or increases the rate of axon extension involved in regeneration. [GOC:dgh, GOC:dph, GOC:jid, GOC:lm]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The process in which a relatively unspecialized cell acquires specialized features of a mechanoreceptor, a cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. [CL:0000199, GOC:jl]
A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Neurotrophins are a family of secreted growth factors that induce the survival, development, and function of neurons. [GOC:bf, GOC:jc, GOC:signaling, PMID:17466268, PR:000021998, Wikipedia:Neurotrophin]
Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine. [GOC:mah]
Any process that initiates the activity of the inactive enzyme protein kinase B. [GOC:pg]
Any process that activates or increases the frequency, rate or extent of cell migration. [GOC:go_curators]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
Any biological process in an organism that recurs with a regularity of approximately 24 hours. [GOC:bf, GOC:go_curators]
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:jid, UBERON:0000948]
A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, GOC:signaling]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
The initiation of the activity of the inactive enzyme MAP kinase (MAPK). [PMID:9561267]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Combining with a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth, and transmitting the signal to initiate a change in cell activity. [GOC:jl, GOC:signaling, http://www.mercksource.com/]
Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate. [EC:2.7.10.1, GOC:mah]
Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. [EC:2.7.10]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Interacting selectively and non-covalently with one of the p53 family of proteins. [GOC:hjd]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The chemical reactions and pathways resulting in the formation of citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins. [ISBN:0198506732]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GOC:go_curators, ISBN:0198547684]
The chemical reactions and pathways resulting in the formation of ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. [GOC:jl, ISBN:0192801023]
The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins. [ISBN:0198506732]
The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid. [GOC:go_curators]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. [GOC:jl]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: L-glutamate 5-semialdehyde + NADP(+) + phosphate = L-glutamyl 5-phosphate + H(+) + NADPH. [EC:1.2.1.41, RHEA:19544]
Catalysis of the reaction: L-glutamate + ATP = L-glutamyl 5-phosphate + ADP + H(+). [EC:2.7.2.11, RHEA:14880]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A series of molecular signals mediated by a steroid hormone binding to a receptor. [PMID:12606724]
Any series of molecular signals initiated by a ligand binding to an receptor located within a cell. [GOC:bf, GOC:mah]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Combining with thyroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. [GOC:signaling]
Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function. [GOC:signaling, PMID:14708019]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin. [ISBN:0198506732]
Any process that activates or increases the frequency, rate or extent of glucose import in response to insulin stimulus. [GOC:BHF]
Any process that activates or increases the frequency, rate or extent of ammonia assimilation cycle. [GOC:BHF]
Any process that activates or increases the frequency, rate or extent of glutamate metabolic process. [GOC:sl]
Any process that modulates the frequency, rate or extent of cholesterol homeostasis. [GOC:BHF]
Any process that activates or increases the frequency, rate or extent of phosphatidic acid biosynthetic process. [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23767959]
Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor secretion. [GO_REF:0000058, GOC:TermGenie, PMID:15560120]
Any process that activates or increases the frequency, rate or extent of adipose tissue development. [GO_REF:0000058, GOC:TermGenie, PMID:23081848]
Any process that stops, prevents or reduces the frequency, rate or extent of interferon-gamma secretion. [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:19109405]
The regulated release of any member of the interleukin-17 family of cytokines from a cell. [GOC:add, GOC:BHF, GOC:mah, http://www.copewithcytokines.de/cope.cgi?key=interleukins]
Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. [CHEBI:35352, GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. [GOC:BHF, GOC:mah]
Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell. [GOC:BHF, GOC:mah]
Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose. [GOC:BHF, GOC:dph]
Any process involved in the maintenance of an internal steady state of fatty acid within an organism or cell. [GOC:BHF, GOC:rl]
Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. [GOC:ai]
Any process that increases the frequency, rate or extent of insulin receptor signaling. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling. [GOC:jl]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. [GOC:jl]
Any process involved in the maintenance of an internal steady state of glucose within an organism or cell. [GOC:go_curators]
A series of molecular signals initiated by a bile acid binding to an receptor located within a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, PMID:10334992]
A series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:signaling, PMID:12016314]
Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose. [GOC:bf, GOC:yaf]
Any process involved in the maintenance of an internal steady state of triglyceride within a cell or between a cell and its external environment. [GOC:BHF]
The modification of histone H3 by addition of a methyl group to arginine at position 17 of the histone. [GOC:mah]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving urea. [GOC:mah]
Any series of molecular signals generated as a consequence of binding to toll-like receptor 9. [GOC:add, PMID:16551253, PMID:17328678]
Any series of molecular signals generated as a consequence of binding to toll-like receptor 4. [GOC:add, PMID:16551253, PMID:17328678]
Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. [GOC:add, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. [GOC:dph, GOC:rl, GOC:tb]
Any process that modulates the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded. [GOC:BHF, GOC:dph, GOC:tb]
Any process that decreases the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor. [GOC:dph, GOC:tb]
The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. [GOC:go_curators]
A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:go_curators, GOC:signaling]
The aggregation, arrangement and bonding together of a set of components to form a junction between cells. [GOC:ai]
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with chenodeoxycholic acid. [GOC:bf, GOC:TermGenie, PMID:10334992]
Interacting selectively and non-covalently with a retinoid X receptor. [GOC:ai]
Combining with a bile acid and transmitting the signal to initiate a change in cell activity. A bile acid is any member of a group of steroid carboxylic acids occurring in bile. [CHEBI:3098, GOC:bf, PMID:10334992, PMID:12718893]
Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile. [GOC:rph]
Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. [GOC:signaling, GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. [GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. [GOC:txnOH]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. [GOC:ai]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. [GOC:ai, GOC:bf]
The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. [GOC:ai, http://www.onelook.com/]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Combining with an odorant and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity in response to detection of smell. [GOC:bf, GOC:dph, GOC:sart, PMID:19135896, PMID:21041441]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. [GOC:ai]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. [GOC:ai, GOC:bf]
The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. [GOC:ai, http://www.onelook.com/]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Combining with an odorant and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity in response to detection of smell. [GOC:bf, GOC:dph, GOC:sart, PMID:19135896, PMID:21041441]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell. [ISBN:0716731363]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule. [GOC:curators]
Endonucleolytic cleavage within ITS2 between the 5.8S rRNA and the LSU-rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. [GOC:curators, PMID:10690410]
Catalysis of the reaction: NTP + 5'-dephosphopolynucleotide = NDP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA. [EC:2.7.1.78]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis, GOC:yaf, PMID:17340152]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell.  Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. [GOC:dos, GOC:mah]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Interacting selectively and non-covalently with the tumor necrosis factor receptor. [GOC:ai]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
Interacting selectively and non-covalently with any protease or peptidase. [GOC:hjd]
An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules. [PMID:11121744]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides. [GOC:vw, http://en.wikipedia.org/wiki/Microtubule_organizing_center, ISBN:0815316194, PMID:17072892, PMID:17245416]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction. [GOC:mgi_curators, PMID:11244041, PMID:11376300]
Any process that activates or increases the frequency, rate or extent of T-helper 2 cell activation. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of T-helper 17 type immune response. [GOC:BHF, GOC:mah]
Any process that activates or increases the frequency, rate or extent of telomere capping. [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:23959892]
Any process that modulates the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules. [GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of T cell death by apoptotic process. [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196]
The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). [GOC:dph]
Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). [GOC:ai]
Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB. [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030]
Any process that activates or increases the frequency, rate or extent of T cell activation. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2. [GOC:go_curators]
Any process that activates or increases the rate or extent of T cell proliferation. [GOC:ai]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
Any process that activates or increases the frequency, rate, or extent of interleukin-4 production. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines. [GOC:add, GOC:mah]
Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase. [GOC:mah]
The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine. [RESID:AA0037]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain). [GOC:jl, http://www.copewithcytokines.de/]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol. [EC:2.7.11.13]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The component of the mitochondrial outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. [GOC:dos, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A positive regulation of the macromitophagy pathway that is triggered by mitochondrial depolarization and requires the function of a parkin-family molecule. [GOC:autophagy, GOC:dph, GOC:pad, GOC:PARL, PMID:25349190]
Any process in which a mitochondrion or mitochondria are transported to, and/or maintained in, a specific location within the cell. [GOC:ai]
Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation. [CL:0000192, GOC:ebc]
The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. [GOC:jid, GOC:mtg_sensu]
Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction. [GOC:bf]
Any process in which a protein is transported to, or maintained at, the pre-autophagosomal structure (PAS). [GOC:rb]
Merging of two or more mitochondria within a cell to form a single compartment. [PMID:11038192]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion. [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein. [GOC:mcc, ISBN:0716731363]
The initial formation of a blastocyst from a solid ball of cells known as a morula. [GOC:dph, ISBN:0124020607, ISBN:0198542771]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway. [GOC:mah]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. [http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit. [GOC:bhm, GOC:vw, PMID:10766736, PMID:16721054, PMID:17079683, PMID:19328067, PMID:7759473]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner. [GOC:krc, PMID:11602261]
Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain. [GOC:TermGenie]
Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation. [GOC:se, GOC:TermGenie, PMID:15121841]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of CDK activity. [GOC:go_curators, GOC:pr]
The process of introducing a phosphate group on to a protein. [GOC:hb]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with a 7SK small nuclear RNA (7SK snRNA). [GOC:nhn, PMID:21853533]
Interacting selectively and non-covalently with an RNA polymerase molecule or complex. [GOC:BHF, GOC:mah, GOC:txnOH]
Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:jl, GOC:txnOH, SO:0005836]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
Interacting selectively and non-covalently with a small nuclear RNA (snRNA). [GOC:mah]
Modulates the activity of a cyclin-dependent protein serine/threonine kinase, enzymes of the protein kinase family that are regulated through association with cyclins and other proteins. [GOC:pr, GOC:rn, PMID:7877684, PMID:9442875]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that stops, prevents or reduces the frequency, rate or extent of synapse maturation. [GOC:mah]
The process in which the vasculature of the retina is generated and organized. [GOC:BHF, GOC:dph]
Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts. [GOC:ai]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Any process that modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:mah]
The area in the center of the anaphase spindle consisting of microtubules, microtubule bundling factors and kinesin motors where the spindle microtubules from opposite poles overlap in an antiparallel manner. [GOC:mtg_cell_cycle, GOC:vw]
Either of the ends of a mitotic spindle, a spindle that forms as part of mitosis, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules. [GOC:vw]
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). [GOC:dph, GOC:jid, GOC:tb, UBERON:0000955]
The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron. [GOC:ai, GOC:mtg_sensu, GOC:sart]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle. [GOC:go_curators, GOC:mah]
The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. [GOC:add, GOC:rl, ISBN:0781735149, PMID:16551251]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. [GOC:mah]
Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules. [GOC:clt]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. [GOC:dph, GOC:tb]
The process in which anatomical structures of the mammary gland buds are generated and organized. Mammary gland buds form by an outpocketing of the mammary placodes and grow to invade the mammary fat, when they form the mammary cord. [GOC:dph, PMID:12558599]
The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel. [GOC:cjm, GOC:mah, GOC:mtg_sensu, PMID:10333884, PMID:15355794]
The process in which the anatomical structures of the hair follicle are generated and organized. [GOC:ln]
Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway. [GOC:go_curators]
Any process that stops, prevents or reduces the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. [GOC:dph, GOC:tb]
Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate. [GOC:go_curators, GOC:isa_complete, ISBN:0521436125]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The lipid bilayer surrounding a synaptic vesicle. [GOC:mah]
The lipid bilayer surrounding a secretory granule. [GOC:mah]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
Any process that modulates the frequency, rate or extent of the regulated release of insulin. [GOC:ai]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:add, ISBN:0121245462, ISBN:0896039986]
Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. [GOC:ai]
Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. [GOC:ai, GOC:dgf]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [ISBN:0198506732]
Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane. [EC:3.6.1.3, GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. [PMID:11687631, PMID:11742990, PMID:11805083, PMID:12488447, PMID:18508253, PMID:18838538]
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone. [GOC:ai, GOC:pr]
Repression of transcription of telomeric DNA by altering the structure of chromatin. [PMID:10219245]
Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein. [PMID:12086618]
The union of male and female gametes to form a zygote. [GOC:ems, GOC:mtg_sensu]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule. [GOC:mah]
Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N6-methyladenine. [EC:2.1.1.55]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
A zone of apposition between the membranes of two organelles, structured by bridging complexes. Membrane contact sites (MCSs) are specialized for communication, including the efficient traffic of small molecules such as Ca2+ ions and lipids, as well as enzyme-substrate interactions. [GOC:jl, PMID:16806880]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. [GOC:dos, GOC:mah]
The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A bundle of cross-linked stereocilia, arranged around a kinocilium on the apical surface of a sensory hair cell (e.g. a neuromast, auditory or vestibular hair cell). Stereocilium bundles act as mechanosensory organelles by responding to fluid motion or fluid pressure changes. [GOC:ecd, PMID:15661519, PMID:7840137]
An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles. [GOC:ecd, PMID:15661519, PMID:7840137]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes. [GOC:cilia, ISBN:0824072820]
The aggregation, arrangement and bonding together of a set of components to form a non-motile cilium. [GO_REF:0000079, GOC:cilia, GOC:kmv, GOC:TermGenie, PMID:14521833, PMID:14521834]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of inner ear receptor cells. [GOC:dph]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of auditory hair cells. [GOC:dph, PMID:10978835]
A reflex process in which an animal immediately tries to turn over after being placed in a supine position. [GOC:dph, PMID:8635460]
The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. [GOC:ai]
The series of events involved in equilibrioception in which a mechanical stimulus is received and converted into a molecular signal. During equilibrioception, mechanical stimuli may be in the form of input from pressure receptors or from the labyrinth system of the inner ears. [GOC:ai, GOC:dos]
The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal. [GOC:ai]
The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure. [GOC:sr]
The process in which a relatively unspecialized cell acquires specialized features of an auditory hair cell. [CL:0000201, GOC:jl]
The increase in size or mass of an entire multicellular organism, as opposed to cell growth. [GOC:bf, GOC:curators, GOC:dph, GOC:tb]
The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg. [GOC:jid, GOC:pr, ISBN:0198606907]
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GOC:dph]
The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. [GOC:ai]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell.  Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. [GOC:dos, GOC:mah]
The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell. [ISBN:0198506732]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. [GOC:mah]
The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. [GOC:dph, GOC:jl, GOC:tb, ISBN:0198506732]
An action or movement due to the application of a sudden unexpected stimulus. [GOC:dph]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A specialized region below the presynaptic membrane, characterized by electron-dense material, a specialized cytoskeletal matrix and accumulated (associated) synaptic vesicles. [GOC:dos]
The part of a synapse that is part of the presynaptic cell. [GOC:dos]
A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix. [GOC:dh, GOC:dl, GOC:ef, GOC:jid, GOC:pr, PMID:3152289]
The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
The specialized, terminal region of a neuron projection such as an axon or a dendrite. [GOC:jl]
A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732]
The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. [GOC:nln, ISBN:0198506732]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A series of molecular signals that conveys information from the presynapse to the nucleus via cytoskeletal transport of a protein from a presynapse to the component to the nucleus where it affects biochemical processes that occur in the nucleus (e.g DNA transcription, mRNA splicing, or DNA/histone modifications). [GOC:dos, PMID:24317321, PMID:25652077]
Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. [GOC:bf]
The aggregation, arrangement and bonding together of a set of components to form a synapse.  This process ends when the synapse is mature (functional). [GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus. [GOC:mtg_sensu, ISBN:0198547684]
The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin. [GOC:dgh, GOC:dph, PMID:11487378]
Any process that modulates the frequency, rate or extent of osteoblast differentiation. [GOC:go_curators]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight. [GOC:jid, GOC:jl]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that modulates the frequency, rate or extent of translational initiation. [GOC:go_curators]
The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA. [ISBN:019879276X]
Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide. [ISBN:0198506732]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2]
A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened. [GOC:mah, PMID:15205520]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions. [GOC:bf, GOC:jl]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. [PMID:16645198, PMID:20044567]
A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi  and Golgi-to-ER transport. [GOC:pr, PMID:16723730]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process leading to the attainment of the full functional capacity of a protein. [GOC:ai]
The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%). [GOC:mah, ISBN:0198506732]
Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix. [GOC:mah, ISBN:0815316194]
Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
The progression of a chondrocyte over time from after its commitment to its mature state where the chondrocyte will contribute to the shaping of an endochondral bone. [GOC:ascb_2009, GOC:dph, GOC:tb]
Interacting selectively and non-covalently with an unfolded protein. [GOC:ai]
Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%). [GOC:ai, ISBN:0198506732]
Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme. [GOC:ai]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. [GOC:dph, GOC:jl, GOC:mah]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
A structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. [GOC:mah, ISBN:0815316194]
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. [GOC:dgh, ISBN:0198506732]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. [GOC:ai]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein. [PMID:10037737, PMID:10068444, PMID:10940390]
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. [ISBN:0198506732]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
Any process that increases the rate of phospholipase C activity. [GOC:dph, GOC:tb]
Any process that increases the concentration of calcium ions in the cytosol. [GOC:ai]
A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, GOC:signaling]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with manganese (Mn) ions. [GOC:ai]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein. [EC:2.7.10.2]
Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. [EC:2.7.10]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Interacting selectively and non-covalently with magnesium (Mg) ions. [GOC:ai]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:go_curators]
The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein. [GOC:go_curators]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues. [GOC:BioGRID, GOC:dph, GOC:mah, GOC:tb, PMID:22863777]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. [GOC:go_curators]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:go_curators]
A membrane-bounded intracellular vesicle as initially formed upon the ingestion of particulate material by phagocytosis. [GOC:mah, PMID:12388753]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. [GOC:mah]
Reactions triggered in response to the presence of a virus that act to protect the cell or organism. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-8. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-beta. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-alpha. [GOC:go_curators]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:jl, ISBN:0198506732]
Any series of molecular signals generated as a consequence of binding to toll-like receptor 7. [GOC:add, PMID:16551253, PMID:17328678]
Any process that activates or increases the frequency, rate, or extent of interleukin-8 production. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of interleukin-6 production. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of chemokine production. [GOC:mah]
The process of introducing a phosphate group into an inhibitor of kappa B (I-kappaB) protein. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing bound NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. [GOC:bf, GOC:jl, PMID:21772278, PMID:7594468]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response. [GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. [GOC:hjd]
Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme. [PMID:15066275, PMID:15066283]
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. [GOC:go_curators, Wikipedia:Transmembrane_receptor]
Interacting selectively and non-covalently with single-stranded RNA. [GOC:jl]
Interacting selectively and non-covalently with double-stranded RNA. [GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that decreases the rate, frequency, or extent of inclusion body assembly. Inclusion body assembly is the aggregation, arrangement and bonding together of a set of components to form an inclusion body. [GOC:BHF, GOC:dph, GOC:tb]
Interacting selectively and non-covalently with a proteasome, a large multisubunit protein complex that catalyzes protein degradation. [GOC:mah]
Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport. [http://www.onelook.com]
Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size. [ISBN:0198506732]
Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons. [GOC:krc, ISBN:0879695897, PMID:9582290]
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
Any process that modulates the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Catalysis of the transfer of a phosphate group from one compound to the 2' position of another. [GOC:jl, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The directed movement of zinc II ions across a membrane into a cell or organelle. [GOC:BHF, GOC:mah]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
Any process that activates or increases the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell. [GOC:ai]
The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell. [GOC:ai, GOC:mah]
Enables the transfer of metal ions from one side of a membrane to the other. [GOC:ai]
Enables the transfer of zinc (Zn) ions from one side of a membrane to the other. [GOC:dgf]
A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, IGF2BP1 and at least four additional proteins: HNRNPU, SYNCRIP, YBX1, and DHX9. [GOC:mah, PMID:19029303]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation. [GOC:jp, PMID:16554824]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
The binding of a cell to the extracellular matrix via adhesion molecules. [GOC:hb]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers. [ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A protein complex formed of four sarcoglycans plus sarcospan; there are six known sarcoglycans: alpha-, beta-, gamma-, delta-, epsilon- and zeta-sarcoglycan; all are N-glycosylated single-pass transmembrane proteins. The sarcoglycan-sarcospan complex is a subcomplex of the dystrophin glycoprotein complex, and is fixed to the dystrophin axis by a lateral association with the dystroglycan complex. [PMID:15117830, PMID:16710609]
A protein complex that includes alpha- and beta-dystroglycan, which are alternative products of the same gene; the laminin-binding component of the dystrophin-associated glycoprotein complex, providing a link between the subsarcolemmal cytoskeleton (in muscle cells) and the extracellular matrix. Alpha-dystroglycan is an extracellular protein binding to alpha-laminin and to beta-dystroglycan; beta-dystroglycan is a transmembrane protein which binds alpha-dystroglycan and dystrophin. [PMID:15117830, PMID:16710609]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. [GOC:dph, GOC:tb]
The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. [GOC:dph]
The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate. [CL:0000187, GOC:devbiol]
The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure. [GOC:dph, GOC:jid, GOC:lm]
The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work. [GOC:jid, ISBN:0198506732]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A multisubunit complex that is located at the replication origins of a chromosome in the nucleus. [GOC:elh]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A multisubunit complex that is located at the replication origins of a chromosome. [GOC:elh]
The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action. [ISBN:071673706X, ISBN:0815316194]
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. [GOC:mah]
Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally. [GOC:curators]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone. [GOC:dph, GOC:vw]
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GOC:go_curators, GOC:rb]
The modification of a protein by cis-trans isomerization of a proline residue. [GOC:krc, PMID:16959570]
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. [ISBN:0198506732]
Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506. [GOC:jl]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0). [EC:5.2.1.8]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:add, ISBN:0781735149]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide. [GOC:dos, GOC:vw]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that maintains the redox environment of a cell or compartment within a cell. [GOC:ai, GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen radical stimulus. An oxygen radical is any oxygen species that carries a free electron; examples include hydroxyl radicals and the superoxide anion. [GOC:krc, ISBN:0124325653]
Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP. [GOC:jl]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds. [MetaCyc:DISULFOXRED-RXN]
Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. [ISBN:0198506732]
Catalysis of the reaction: NADP(+) + thioredoxin = H(+) + NADPH + thioredoxin disulfide. [EC:1.8.1.9, RHEA:20348]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:add, ISBN:0781735149]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:add, ISBN:0781735149]
A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids. [GOC:BHF, GOC:mah, PMID:16373184]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A protein complex produced by sequentially activated components of the complement cascade inserted into a target cell membrane and forming a pore leading to cell lysis via ion and water flow. [GOC:add, ISBN:0198547684, ISBN:068340007X, ISBN:0781735149]
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer. [GOC:ai]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. [GOC:add]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A protein complex that can methylate lysine-4 of histone H3, and which contains either of the protein subunits MLL3 or MLL4 in mammals, or equivalent in other species. [GOC:sart, PMID:21875999]
A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins. [GOC:bf]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone. [GOC:ai, GOC:pr]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein. [PMID:12086618]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the transfer of a methyl group to an acceptor molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A protein complex that forms part of a proton-transporting two-sector ATPase complex and catalyzes ATP hydrolysis or synthesis. The catalytic domain (F1, V1, or A1) comprises a hexameric catalytic core and a central stalk, and is peripherally associated with the membrane when the two-sector ATPase is assembled. [GOC:mah, PMID:10838056]
The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis. [GOC:mah, GOC:vw]
Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism. [EC:3.6.3.14]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that stops, prevents or reduces the frequency, rate or extent of glucose import in response to insulin stimulus. [GOC:BHF]
Any process that activates or increases the frequency, rate or extent of ATP biosynthetic process. [GOC:obol]
Any process that stops, prevents or reduces the frequency, rate or extent of ATP biosynthetic process. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process. [GOC:mah]
Any process that modulates the frequency, rate or extent of reactive oxygen species metabolic process. [GOC:mah]
Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle. [GOC:mtg_cell_cycle]
Any process that decreases the rate, frequency or extent of the process in which new strands of DNA are synthesized in the mitochondrion. [GOC:tb]
Any process that decreases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane. [GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-6 stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus. [GOC:mah]
The process in which the anatomical structures of a mitochondrion are generated and organized. [GOC:mah]
Any process that activates or increases the rate or extent of fat cell proliferation. [GOC:mah, GOC:sl]
Any process that modulates the establishment or extent of the mitochondrial membrane potential, the electric potential existing across the mitochondrial membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a leptin stimulus. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. It plays a key role in regulating energy intake and energy expenditure, including appetite and metabolism. [GOC:yaf]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures. [PMID:10754561]
The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. [GOC:dos, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells. [GOC:mtg_muscle, PMID:11732910]
A sodium channel in a cell membrane whose opening is governed by the membrane potential. [ISBN:0198506732]
Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity. [GOC:obol]
A cardiac conduction process that modulates the frequency or rate of heart contraction. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
An action potential that occurs in an atrioventricular node cardiac muscle cell. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
The process in which cardiac muscle cell membrane potential changes in the depolarizing direction from the negative resting potential towards the positive membrane potential that will be the peak of the action potential. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
An action potential that occurs in a cardiac muscle cell and is involved in its contraction. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
Any process that modulates the establishment or extent of a membrane potential in the polarizing direction towards the resting potential in a ventricular cardiomyocyte. [GOC:BHF, GOC:dph, GOC:mtg_cardiac_conduct_nov11, GOC:tb]
Any process that modulates the potential difference across a post-synaptic membrane. [GOC:dph, GOC:ef]
Muscle contraction of cardiac muscle tissue. [GOC:dph]
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:vw]
Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:dph, GOC:tb]
The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Enables the transmembrane transfer of a sodium ion by a voltage-gated channel through the plasma membrane of a cardiac muscle cell contributing to the depolarization phase of an action potential. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient. [GOC:BHF, GOC:jl]
Modulates the activity of a sodium channel. [GOC:mah]
Enables the transmembrane transfer of a sodium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0815340729]
A complex consisting of methionyl- and glutamyl-tRNA synthetases. The tRNA synthetases present in the complex bind to their cognate tRNAs more efficiently than they do as monomers. [GOC:mcc, PMID:11069915]
A multienzyme complex found in all multicellular eukaryotes composed of eight proteins with aminoacyl-tRNA synthetase activities (abbreviated as: ArgRS, AspRS, GluProRS, GlnRS, IleRS, LeuRS, LysRS, MetRS where RS is the enzyme, preceded by the amino acid it uses as a substrate) as well as three non-synthetase proteins (p43, p38, and p18) with diverse functions. Several of these subunits are known dimers, so the total polypeptide count in the multisynthetase complex is at least fifteen. All of the enzymes in this assembly catalyze the same reaction, the covalent attachment of an amino acid to either the 2'- or 3'-hydroxyl of the 3'-terminal adenosine of tRNA, but using different substrates. [GOC:jl, PMID:16169847]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis. [GOC:ma]
Functions to control the survival, growth, differentiation and effector function of tissues and cells. [ISBN:0198599471]
Interacting selectively and non-covalently with transfer RNA. [GOC:ai]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
An adherens junction which connects a cell to another cell. [GOC:hb]
The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). [GOC:dgh, GOC:jid]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The action of a molecule that contributes to the structural integrity of a muscle fiber. [GOC:mah]
Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules. [GOC:clt]
Interacting selectively and non-covalently with vinculin, a protein found in muscle, fibroblasts, and epithelial cells that binds actin and appears to mediate attachment of actin filaments to integral proteins of the plasma membrane. [ISBN:0721662544]
Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class. [GOC:go_curators, Pfam:PF00017]
Interacting selectively and non-covalently with alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats. [PMID:10984498, PMID:11699871, PMID:15014165]
The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells. [GOC:jl]
The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain). [GOC:jl, http://www.copewithcytokines.de/]
The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:ai]
A cytoskeleton organization process that directly or indirectly links cytoskeletal filaments to the plasma membrane. [ISBN:0198599323]
Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. [GOC:dph, GOC:tb]
Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. [GOC:BHF, GOC:dph, GOC:tb]
The process aimed at the progression of a Schwann cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function. [GOC:dgh, GOC:ef]
The process in which a virus effects a change in the structure or processes of its host organism. [GOC:bf, GOC:jl, ISBN:0781718325, UniProtKB-KW:KW-0945]
A developmental process, independent of morphogenetic (shape) change, that is required for a nerve to attain its fully functional state. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. [GOC:go_curators]
Any process in which a microtubule is maintained in a specific location in a cell. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B. [GOC:ai]
The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. [GOC:dph, GOC:mtg_lung]
The process in which the branching structure of the salivary gland is generated and organized. [GOC:dph]
The process in which the migration of an axon growth cone of a commissural neuron is directed to its target in the brain in response to a combination of attractive and repulsive cues. [GOC:BHF, GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of basement membrane assembly involved in embryonic body morphogenesis. [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:23940118]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. [GOC:dgh, GOC:hb, GOC:mah]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. [GOC:md, GOC:mtg_sensu, ISBN:0135712254]
A multiprotein complex that forms a strong mechanical link between the cytoskeleton and extracellular matrix; typical of, but not confined to, muscle cells. The complex is composed of transmembrane, cytoplasmic, and extracellular proteins, including dystrophin, sarcoglycans, dystroglycan, dystrobrevins, syntrophins, sarcospan, caveolin-3, and NO synthase. [PMID:15117830, PMID:16710609]
A protein complex that includes alpha- and beta-dystroglycan, which are alternative products of the same gene; the laminin-binding component of the dystrophin-associated glycoprotein complex, providing a link between the subsarcolemmal cytoskeleton (in muscle cells) and the extracellular matrix. Alpha-dystroglycan is an extracellular protein binding to alpha-laminin and to beta-dystroglycan; beta-dystroglycan is a transmembrane protein which binds alpha-dystroglycan and dystrophin. [PMID:15117830, PMID:16710609]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments. [ISBN:0815316194]
A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. [GOC:mah, GOC:pr, ISBN:0815316194]
An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed. [GOC:mh]
The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers. [ISBN:0198506732]
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. [PMID:16645198, PMID:20044567]
The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A cytoskeletal structure composed of filamentous protein that forms beneath the membrane of many cells or organelles, in the plane of cell or organelle division. Ring contraction is associated with centripetal growth of the membrane that divides the cytoplasm of the two daughter cells or organelles. [GOC:mah, ISBN:0123645859, ISBN:0792354923, PMID:10791428, PMID:17913889]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. [GOC:go_curators]
A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. [GOC:dph, GOC:ef, GOC:jid, GOC:lm, GOC:mtg_muscle]
The process in which a relatively unspecialized cell acquires the specialized features of a glial cell. [GOC:go_curators, GOC:mtg_sensu]
The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. [GOC:bf, GOC:jid, ISBN:0582227089]
The series of successive proteolytic cleavages of the Notch protein, which result in an active form of the receptor. [PMID:12651094, PMID:14986688]
Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor. [GOC:ceb]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of striated muscle cell differentiation. [CL:0000737, GOC:ai]
The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways. [GOC:mtg_lung, PMID:9751757]
Any process that activates or increase the rate of skeletal muscle regeneration. [GOC:jl]
Any process that modulates the frequency, rate or extent of protein binding. [GOC:go_curators]
The modification of histones by removal of acetyl groups. [GOC:ai]
Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. [GOC:dph, GOC:go_curators, GOC:tb]
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:jid, UBERON:0000948]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell. [GOC:dph, ISBN:0124020607, ISBN:0198542771]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The regulated release of immunoglobulins from a B cell or plasma cell, whose mechanism includes the use of alternate polyadenylylation signals to favor the biosynthesis of secreted forms of immunoglobulin over membrane-bound immunoglobulin. [GOC:add, ISBN:0781735149, PMID:9185563]
Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. [GOC:jl]
An immune response mediated through a body fluid. [GOC:hb, ISBN:0198506732]
Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication. [GOC:add, GOC:dph, GOC:tb, ISBN:0781735149]
Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. [CL:0000236, GOC:add, GOC:mtg_apoptosis, ISBN:0781735149]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:mah]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues. [GOC:BioGRID, GOC:dph, GOC:mah, GOC:tb, PMID:22863777]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins. [GOC:vp]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group. [GOC:jl, ISBN:0198506732]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of sodium-dependent phosphate transport. [GOC:BHF]
Any process that stops, prevents, or reduces the frequency, rate or extent of non-canonical Wnt signaling pathway. [GOC:obol, GOC:yaf]
Any process that activates or increases the frequency, rate or extent of keratinocyte apoptotic process. [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, GOC:TermGenie, PMID:18938133]
Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. [GOC:tb]
Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. [GOC:dph, GOC:tb]
The process in which bones are generated and organized. [GOC:dph]
Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell. [GOC:jid, GOC:mah]
Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway. [GOC:mah]
The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state. [GOC:dph, GOC:go_curators, PMID:11532397]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
Any process that activates or increases the frequency, rate or extent of receptor internalization. [GOC:hjd]
Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling. [GOC:jl]
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. [GOC:lh]
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. [GOC:ai, GOC:mah, ISBN:08789310662000]
The controlled release of proteins from a cell. [GOC:ai]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The area in the center of the spindle where the spindle microtubules from opposite poles overlap. [GOC:ai, PMID:15296749]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue. [GOC:mah, ISBN:0815316194]
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. [PMID:16645198, PMID:20044567]
Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:go_curators]
Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines. [GOC:nln]
A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse.  They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including \thin\, \stubby\, \mushroom\, and \branched\, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity. [GOC:nln]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A cytoskeleton-like structure, originating from the basal body at the proximal end of a cilium, and extending proximally toward the cell nucleus. Rootlets are typically 80-100 nm in diameter and contain cross striae distributed at regular intervals of approximately 55-70 nm. [GOC:cilia, PMID:12427867]
The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential. [GOC:nln]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. [GOC:nln, ISBN:0198506732]
A vesicle that mediates transport from the endoplasmic reticulum to the Golgi complex; bears a coat formed of the COPII coat complex proteins; such vesicles found associated with endoplasmic reticulum (ER) membranes at steady state, and are involved in ER to Golgi (anterograde) vesicle transport. [GOC:ascb_2009, GOC:dph, GOC:mah, GOC:tb, PMID:11252894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. [GOC:dgh, GOC:hb, GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER. [ISBN:0198506732]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide. [GOC:ai]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The generation of amyloid fibrils, insoluble fibrous protein aggregates exhibiting beta sheet structure, from proteins. An example of this is seen when human RIP1 and RIP3 kinases form a heterodimeric functional amyloid signaling complex (PMID:22817896). [GOC:cvs, GOC:jj, GOC:ppm, GOC:sj, PMID:16533927, PMID:21148556, PMID:22817896]
Any process involved in the maintenance of an internal steady state of calcium ions within the smooth endoplasmic reticulum of a cell or between the smooth endoplasmic reticulum and its surroundings. [GOC:ai, GOC:mah]
Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. [CL:0000540, GOC:mtg_apoptosis, MeSH:A.08.663]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. [GOC:ai]
The growth of a synapse at a neuromuscular junction, the site of apposition of a motor end plate and the subneural cleft of the skeletal muscle fiber that it innervates. [ISBN:0721662544]
Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors. [GOC:ai, GOC:dph, http://www.onelook.com/]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). [GOC:ai, GOC:pr]
Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). [GOC:ai]
The process in which outgrowths develop from the axons of intact undamaged neurons. [GOC:dgh, GOC:dph, GOC:jid, GOC:lm]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. [GOC:dph, GOC:go_curators, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of protein binding. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size. [GOC:dph, GOC:ems, GOC:tb]
A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription. [GOC:signaling, ISBN:0198506732]
The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:mah]
The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions). [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=forebrain]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. [GOC:mah]
The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell. [GOC:jl, ISBN:0198506732]
The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development. [GOC:hb]
The recognition of molecules at the central nervous system midline choice point by an axon growth cone; this choice point determines whether the growth cone will cross the midline. [PMID:11376484]
Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle. [GOC:dph, GOC:mtg_cell_cycle, GOC:tb]
Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. [GOC:go_curators, GOC:isa_complete]
Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue. [GOC:jid, ISBN:0582227089]
Locomotory behavior in a fully developed and mature organism. [GOC:ai]
The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. [ISBN:0198506732]
The directed movement of organelles or molecules along microtubules in neuron projections. [ISBN:0815316194]
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GOC:dph]
The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. [GOC:ai, GOC:dph]
The acquisition and processing of information and/or the storage and retrieval of this information over time. [GOC:jid, PMID:8938125]
De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon. [GOC:dph, GOC:jid, GOC:pg, GOC:pr, ISBN:0198506732]
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
Any process that modulates the frequency, rate or extent of EGF-activated receptor activity. [GOC:dph, GOC:go_curators]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl, PMID:12115731]
A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. [GOC:mah, ISBN:0198506732, ISBN:0716731363]
Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell. [GOC:ai, GOC:mah]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript. [ISBN:0198506732]
Specific behavior of a newborn or infant mammal that results in the derivation of nourishment from the breast. [GOC:dph, GOC:pr]
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
Interacting selectively and non-covalently with a phosphotyrosine-binding (PTB) domain of a protein. [Pfam:PF02174.5, PMID:15924411]
Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver. [ISBN:0198506732]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB. [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues. [GOC:BioGRID, GOC:dph, GOC:mah, GOC:tb, PMID:22863777]
Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. [GOC:BioGRID, GOC:jh2, PMID:9635407]
Any vesicle that is part of the extracellular region. [GO_REF:0000064, GOC:pm, GOC:TermGenie, PMID:24769233]
A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids. [GOC:BHF, GOC:mah, PMID:16373184]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues. [GOC:jl, GOC:rl, http://biotech.icmb.utexas.edu/search/dict-search.html, PMID:10580165]
A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:pde, GOC:rl]
A triglyceride-rich lipoprotein particle that typically contains APOB100, APOE and APOCs and has a density of 1.006-1.019 g/ml and a diameter of between 25-30 nm. IDL particles are found in blood and are formed by the delipidation of very-low-density lipoprotein particles (VLDL). IDL particles are removed from blood by the liver, following binding to the APOE receptor, or are converted to low-density lipoprotein (LDL). [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
A structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of lipid transport across blood brain barrier. [GO_REF:0000058, GOC:sjp, GOC:TermGenie, PMID:24345162]
Any process that activates or increases the frequency, rate or extent of phospholipid efflux. [GO_REF:0000058, GOC:sjp, GOC:TermGenie, PMID:12042316]
Any process that activates or increases the frequency, rate or extent of dendritic spine maintenance. [GO_REF:0000058, GOC:sjp, GOC:TermGenie, PMID:24328732]
Any process that stops, prevents or reduces the frequency, rate or extent of beta-amyloid formation. [GOC:hjd, GOC:TermGenie, PMID:22992957]
Any process that stops, prevents or reduces the frequency, rate or extent of presynaptic membrane organization. [GOC:TermGenie, PubMed:22426000]
Any process that activates or increases the frequency, rate or extent of postsynaptic membrane organization. [GOC:TermGenie, PubMed:22426000]
Any process that stops, prevents or reduces the frequency, rate or extent of neuron death. [GOC:rph, GOC:TermGenie]
Any process that stops, prevents or reduces the frequency, rate or extent of long-term synaptic potentiation. [GOC:BHF, GOC:TermGenie]
Any process that modulates the frequency, rate or extent of beta-amyloid clearance. [GOC:BHF, GOC:TermGenie]
Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide. [GOC:dos, GOC:vw]
The receptor clustering process in which N-methyl-D-aspartate (NMDA) receptors are localized to distinct domains in the cell membrane. [GOC:BHF, GOC:sjp, PMID:15620359]
The glutamate receptor clustering process in which alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors are localized to distinct domains in the cell membrane. [GOC:BHF, GOC:pr, GOC:sjp, PMID:12796785]
Any process involved in the maintenance of internal levels of plasma lipoprotein particles within an organism. [GOC:BHF]
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving triglyceride, any triester of glycerol. [GOC:dph, GOC:sl, GOC:tb]
Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. [GOC:dph, GOC:tb]
The process whose specific outcome is the progression of the cardiovascular system over time, from its formation to the mature structure. The cardiovascular system is the anatomical system that has as its parts the heart and blood vessels. [GOC:mah, UBERON:0004535]
Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell. [GOC:BHF, GOC:mah]
Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. [GOC:dph]
Any process involved in the maintenance of an internal steady state of fatty acid within an organism or cell. [GOC:BHF, GOC:rl]
Any process involved in the maintenance of an internal steady state of lipid within an organism or cell. [GOC:BHF, GOC:rl]
Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of membrane protein ectodomain peptidolysis. [GOC:ai]
Any process that activates or increases the activity of the enzyme nitric-oxide synthase. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. [GOC:ai]
The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs. [GOC:dsf, PMID:16740480]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of endocytosis. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol. [GOC:go_curators]
A process in which a host organism activates or increases the frequency, rate or extent of the release of a process being mediated by a virus with which it is infected. [GOC:jl]
The directed movement of peripheral cell cholesterol, cholest-5-en-3-beta-ol, towards the liver for catabolism. [GOC:ecd, PMID:7751809]
Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity. [GOC:dph, GOC:go_curators]
Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell. [GOC:go_curators]
An increase in the internal diameter of blood vessels, especially arterioles or capillaries, due to relaxation of smooth muscle cells that line the vessels, and usually resulting in a decrease in blood pressure. [GOC:pr, ISBN:0192800981]
The chemical reactions and pathways resulting in the breakdown of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids. [ISBN:0198506732]
The chemical reactions and pathways involving any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids. [ISBN:0198506732]
The process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded. [GOC:BHF, GOC:rl]
The process in which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded. [GOC:BHF, GOC:mah]
The process in which a chylomicron remnant is removed from the blood via receptor-mediated endocytosis into liver cells and its constituent parts degraded. [GOC:BHF, GOC:mah, GOC:pde]
The aggregation and arrangement of proteins and lipids to form a high-density lipoprotein particle. [GOC:BHF, GOC:mah]
The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
The acquisition, loss or modification of a protein or lipid within a very-low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase or lipoprotein lipase and the subsequent loss of free fatty acid. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:rl]
The directed movement of a phospholipid out of a cell or organelle. [GOC:mah]
The directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle. [GOC:sart]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of low-density lipoprotein particle receptors. [GOC:mah]
Any process that modulates the frequency, rate or extent of Cdc42 protein signal transduction. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cGMP. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation. [GOC:mah]
Any intracellular signal transduction in which the signal is passed on within the cell via cyclic GMP (cGMP). Includes production of cGMP, and downstream effectors that further transmit the signal within the cell. [GOC:signaling]
A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed. [ISBN:0121585336]
The targeting and directed movement of proteins into a cell or organelle.  Not all import involves an initial targeting event. [GOC:ai]
The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. [CHEBI:15904, GOC:ai]
Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
The directed movement of lipids into cells that is part of their accumulation and maintenance. [GOC:BHF, GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of cholesterol efflux. Cholesterol efflux is the directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle. [GOC:BHF, GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of cholesterol esterification. Cholesterol esterification is the lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle. [GOC:BHF, GOC:dph, GOC:tb]
Any process that decreases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. [GOC:BHF, GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. [ISBN:0198506732]
Any intracellular signal transduction in which the signal is passed on within the cell via nitric oxide (NO). Includes synthesis of nitric oxide, receptors/sensors for nitric oxide (such as soluble guanylyl cyclase/sGC) and downstream effectors that further transmit the signal within the cell. Nitric oxide transmits its downstream effects through either cyclic GMP (cGMP)-dependent or independent mechanisms. [GOC:jl, PMID:21549190]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl, PMID:12115731]
An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles. [GOC:mah, ISBN:0716731363]
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. [GOC:ceb, GOC:mah]
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [ISBN:0198506732]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. [GOC:ai]
The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins. [ISBN:0198506732]
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
The physiological process in which dietary excess is sensed by the central nervous system, resulting in a reduction in food intake and increased energy expenditure. [GOC:pg, GOC:pr, PMID:12161655]
Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation. [GOC:add]
Interacting selectively and non-covalently with a lipoprotein particle. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. [CHEBI:6495, GOC:BHF, GOC:mah]
Interacting selectively and non-covalently with a very-low-density lipoprotein receptor. [GOC:BHF, GOC:mah]
Increases the activity of phosphatidylcholine-sterol O-acyltransferase, an enzyme that converts cholesterol and phosphatidylcholine (lecithins) to cholesteryl esters and lyso-phosphatidylcholines. [GOC:BHF, GOC:dph, GOC:tb, PMID:4335615]
Interacting selectively and non-covalently with a low-density lipoprotein receptor. [GOC:ai]
Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS. [GOC:jid]
The formation of bonds from two or more atoms within the same ligand to a metal atom in complexes in which the metal is part of a ring. [ISBN:0198506732, ISBN:0716731363]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Enables the directed movement of cholesterol into, out of or within a cell, or between cells. Cholesterol is the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. [GOC:ai]
Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage. [ISBN:0198506732]
Interacting selectively and non-covalently with a lipid. [GOC:ai]
Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester. [ISBN:0198506732]
Enables the directed movement of lipids into, out of or within a cell, or between cells. [GOC:ai]
Interacting selectively and non-covalently with beta-amyloid peptide/protein and/or its precursor. [GOC:hjd]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase. [GOC:curators, ISBN:0815316194]
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups. [ISBN:0198506732]
The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments. [GOC:mah, PMID:11687502, PMID:14754507]
The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes. [GOC:go_curators]
The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group. [ISBN:0198506732]
Catalysis of the reaction: H2O + a medium-chain acyl-CoA = a medium-chain carboxylate + CoA. A medium chain is a chain of between eight and twelve carbons in length. [EC:3.1.2.19]
Catalysis of the reaction: acyl-CoA + H2O = CoA + a carboxylate. [EC:3.1.2.20, MetaCyc:ACYL-COA-HYDROLASE-RXN]
Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate. [EC:3.1.2.2]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane. [GOC:dph, GOC:jid, GOC:kmv, GOC:rph, PMID:10930469, PMID:15601896, PMID:16246101, PMID:21556374, PMID:21562044]
A complex which usually consists of three components, e.g. in Xenopus and yeast, the export receptor CRM1 (also known as exportin 1), the Ran protein and any RNA with a nuclear export sequence (NES). The complex acts to export RNA molecules with a NES from the nucleus through a nuclear pore. [GOC:jl, PMID:9323123]
A structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis. [ISBN:0815316194]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle. [ISBN:0198547684]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. [GOC:elh, PMID:20404130]
A process in which a protein is transported to, or maintained in, a location within a nucleolus. [GOC:TermGenie, PMID:22809626]
The directed movement of a protein across a membrane by means of some agent such as a transporter or pore. [GOC:mah, GOC:vw]
A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell. [GOC:mah]
Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of protein binding. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. [GOC:dph, GOC:jl, GOC:mah]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The directed movement of molecules between the nucleus and the cytoplasm. [GOC:go_curators]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
The directed movement of a protein from the nucleus into the cytoplasm. [GOC:jl]
The directed movement of a protein from the cytoplasm to the nucleus. [GOC:jl]
A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope. [GOC:curators, ISBN:0198506732, PMID:14570049, PMID:9126736]
The directed movement of a ribosomal small subunit from the nucleus into the cytoplasm. [GOC:mah]
The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm. [GOC:mah]
Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA. [PMID:18951094]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate. [GOC:ai]
Enables the transfer of a protein from one side of a membrane to the other. [GOC:jl]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
A prolongation or process extending from a cell, e.g. a flagellum or axon. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments. [ISBN:0815316194]
A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome. [PMID:11019806, PMID:12186635, PMID:14570571]
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. [GOC:dgh, GOC:hb, GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork. [ISBN:0124325653]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria. [GOC:ai]
A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell. [GOC:add]
Any process that activates or increases angiogenesis. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels. [GOC:go_curators]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions. [GOC:signaling]
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, http://en.wikipedia.org/wiki/Cell_migration]
The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of epithelial cell migration. [GOC:BHF, GOC:dph, GOC:tb]
The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester. [ISBN:0198506732]
A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, PR:000006933]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. [GOC:go_curators, GOC:mtg_sensu]
Interacting selectively and non-covalently with a glutamate receptor. [GOC:bf]
Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity. [GOC:mah]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. [EC:3.1.4, GOC:curators]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Interacting selectively and non-covalently with the neurotrophin TRKA receptor. [GOC:ai]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1,2-diacylglycerol + 1D-myo-inositol 1,4,5-trisphosphate + H(+). [EC:3.1.4.11, RHEA:23915]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
An adherens junction which connects a cell to another cell. [GOC:hb]
The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). [GOC:dgh, GOC:jid]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling]
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:add, ISBN:0721601464]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function. [GOC:jl, http://lookwayup.com/]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome. [ISBN:0124325653, ISBN:0198506732]
Any process that stops, prevents or reduces the frequency, rate or extent of serine-type endopeptidase activity. [GOC:TermGenie]
The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa. [GOC:BHF, GOC:mah, UBERON:0001343]
Any process that modulates the frequency, rate or extent of the acrosome reaction. [GOC:dph]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). [GOC:tb, ISBN:0198506732]
The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure. [GOC:jid]
The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. [GOC:dph, GOC:go_curators]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
The multiplication or reproduction of male germ cells, resulting in the expansion of a cell population. [GOC:hjd]
Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme. [GOC:ai]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane. [GOC:mah]
The attachment of one cell to another cell affecting gastrulation. [GOC:dsf, PMID:19091770]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression). [GOC:jl, http://www.cellmigration.org/, ISBN:0878932437]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. [GOC:go_curators, ISBN:0582227089]
Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue. [GOC:jid, ISBN:0582227089]
A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. [GOC:curators, ISBN:9780878933846]
The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through inhibition of adenylyl cyclase activity and a subsequent decrease in the concentration of cyclic AMP (cAMP). [GOC:dph, GOC:mah, GOC:signaling, GOC:tb, ISBN:0815316194]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism. [GOC:dph, UBERON:0002409]
The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. [GOC:go_curators, GOC:mtg_sensu]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [GOC:mah]
Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:kd, GOC:mah]
Interacting selectively and non-covalently with a G-protein alpha subunit. The alpha subunit binds a guanine nucleotide. [GOC:hjd]
The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane. [GOC:dos, GOC:mah]
The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the cytoplasmic side of the membrane. [GOC:dos, GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The lipid bilayer surrounding a late endosome. [GOC:pz]
The lipid bilayer surrounding a vesicle associated with the Golgi apparatus. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center. [NIF_Subcellular:nlx_subcell_20090702, PMID:11964142, PMID:2557062]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. [GOC:ai]
The proteolytic cleavage of a transmembrane protein leading to the release of its intracellular or ecto-domains. [GOC:pde]
The proteolytic cleavage of a transmembrane protein leading to the release of an intracellular domain. [PMID:12808018]
The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain). [GOC:jl, http://www.copewithcytokines.de/]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain, occurring within a membrane. [GOC:jl, ISBN:0198506732]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile. [ISBN:0198506732]
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/]
Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane. [GOC:mtg_muscle, ISBN:0815316194]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, ISBN:0815316194]
The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. [ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation. [GOC:obol]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their own peptide bonds. [GOC:yaf, PMID:18676612, PMID:19144634]
A process in which a protein is transported to, or maintained in, a specific location in a membrane. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus. [GOC:mah]
A cell cycle arrest process that results in arrest during G1 phase, whereupon the cell enters G0 phase, in the context of cell differentiation. [GOC:mah, ISBN:0815316194]
The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms. [GOC:dph]
Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB. [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. [CL:0000056, GOC:go_curators, GOC:mtg_muscle]
The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. [GOC:bf]
Any process that modulates I-kappaB kinase/NF-kappaB signaling. [GOC:jl, PMID:12773372]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of SUMO groups to a protein. [GOC:mah]
Formation of myofibrils, the repeating units of striated muscle. [GOC:mah]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muscle activity stimulus. [GOC:mtg_muscle]
Any process that activates, maintains or increases the frequency, rate or extent of activation of satellite cell involved in skeletal muscle regeneration. The activation of satellite cell is the process that initiates satellite cell division by causing it to move from quiescence to the G1 stage of the cell cycle. The cell swells and there are a number of other small changes. The cells then start to divide. Following cell division the cells will differentiate. [GOC:mtg_muscle]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
The aggregation, arrangement and bonding together of a set of components to form a protein complex. [GOC:ai]
A programmed cell death process observed in bacteria and filamentous fungi and leading to spontaneous death by lysis. Examples are lysis of the mother cell during sporulation of Bacillus subtilis and self-degradation of fungal cells in Aspergillus nidulans. Autolysis is also involved in bacterial biofilm formation. [GOC:add, GOC:jh2, GOC:mtg_apoptosis, PMID:10974124, PMID:19286987, PMID:26811896]
Modulates the activity of a ligase. [GOC:BHF, GOC:rl]
A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex. [GOC:mah, GOC:vw]
Interacting selectively and non-covalently with titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively. [GOC:mah, PMID:10481174]
Interacting selectively and non-covalently with sodium ions (Na+). [GOC:mah]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
The action of a molecule that contributes to the structural integrity of a muscle fiber. [GOC:mah]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium. [GOC:mah]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
Any process that activates or increases the rate of ATP hydrolysis by an ATPase. [GOC:mah]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism. [GOC:lr]
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GOC:go_curators, GOC:rb]
Interacting selectively and non-covalently with an unfolded protein. [GOC:ai]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock. [GOC:mah, GOC:vw]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [GOC:go_curators]
Any process that maintains the redox environment of a cell or compartment within a cell. [GOC:ai, GOC:dph, GOC:tb]
The large subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule. [GOC:curators]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine. [GOC:bf]
The process of removing one or more phosphoric (ester or anhydride) residues from a molecule. [ISBN:0198506732]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. [EC:3.1.3, EC:3.1.3.41, GOC:curators, GOC:pg]
Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate. [GOC:mah]
Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate. [EC:3.1.3.48]
A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of  the core TFIIH complex and the TFIIK complex. [GOC:ew, GOC:krc, PMID:14500720, PMID:22308316, PMID:22572993, PMID:7813015]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD. [GOC:ew, GOC:krc, PMID:14500720, PMID:17215295, PMID:22308316, PMID:22572993, PMID:23028141, PMID:7813015]
The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex. [GOC:krc, GOC:mah, PMID:17079683]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter. [GOC:jl, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts). [PMID:10197977]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats. [EC:2.7.11.23, GOC:mah]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction. [EC:3.6.1.3, GOC:jl]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids. [GOC:BHF, GOC:mah, PMID:16373184]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. [CL:0000034, GOC:isa_complete]
Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway. [GOC:add, ISBN:0781735149]
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium. [GOC:jid, PMID:10485905]
Interacting selectively and non-covalently with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages. [GOC:jl, http://lookwayup.com/]
Interacting selectively and non-covalently with interleukin-1. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with interleukin-8. [GOC:jl]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate. [GOC:curators]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme. [GOC:ai]
Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides. [GOC:jl]
Interacting selectively and non-covalently with any protease or peptidase. [GOC:hjd]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein. [GOC:jl, PMID:11265250]
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:add, ISBN:0781735149]
A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation. [GOC:dos, GOC:go_curators, PMID:19028679, PMID:20054389, PMID:6305978]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. [GOC:txnOH]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The directed movement of a protein to a specific location in the plasma membrane. [GOC:dph, GOC:tb]
Any process leading to the attainment of the full functional capacity of a protein. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway. [GOC:go_curators]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme. [GOC:ai]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. [ISBN:0198547684]
A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus. [GOC:mtg_sensu, ISBN:0198547684]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. [GOC:mah]
Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules. [GOC:dph, GOC:pf, GOC:tb]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane. [PMID:10099709, PMID:12563290]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The increase in size or mass of an entire multicellular organism, as opposed to cell growth. [GOC:bf, GOC:curators, GOC:dph, GOC:tb]
The regulated release of gamma-aminobutyric acid by a cell or a tissue. The gamma-aminobutyric acid is the principal inhibitory neurotransmitter in the brain but is also found in several extraneural tissues. [GOC:ef]
The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system. [GOC:ef]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GOC:dph]
The vesicular release of classical neurotransmitter molecules from a neuron, across a chemical synapse, the subsequent activation of neurotransmitter receptors of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. [GOC:jl, MeSH:D009435]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
The aggregation, arrangement and bonding together of a set of components to form a protein complex. [GOC:ai]
The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. [GOC:go_curators, GOC:mtg_sensu]
Interacting selectively and non-covalently with beta-amyloid peptide/protein and/or its precursor. [GOC:hjd]
A protein complex that localizes to interphase centrosomes and to mitotic spindle tubules and regulates mitotic spindle assembly and centrosome integrity; in human, the complex consists of eight subunits, some of which are homologous to subunits of the Drosophila Augmin complex. [PMID:19427217]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized. [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart. [GOC:ai, GOC:expert_rg, GOC:mtg_sensu, GOC:tb]
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. [ISBN:0879693568]
A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules. [GOC:clt]
Any process that activates or increases the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells. [GOC:mah]
The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. [ISBN:0198547684]
Any process that activates or increases the frequency, rate or extent of cell division. [GOC:ai]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
Any process that activates or increases the frequency, rate or extent of signal transduction. [GOC:sm]
A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, GOC:signaling]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68). [GOC:mah, GOC:so]
The binding activity of a molecule that brings together a transmembrane receptor protein tyrosine kinase and one or more other molecules, permitting them to function in a coordinated way. [GOC:mtg_MIT_16mar07, PMID:10502414, PMID:20565848]
The portion of the plasma membrane surrounding a cilium. [GOC:cilia, GOC:dph, GOC:rph]
A prolongation or process extending from a cell, e.g. a flagellum or axon. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. [GOC:cilia, GOC:clt, PMID:21750193]
A ciliary protein complex involved in cilium biogenesis. It consists of at least seven Bardet-Biedl syndrome (BBS) proteins and BBIP10. It moves in association with IFT trains through cilia (likely as an IFT-A/B adaptor or cargo), and is required for the integrity of IFT-A and IFT-B. [GOC:BHF, GOC:cilia, PMID:15231740, PMID:17574030, PMID:26498262]
An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles. [GOC:ecd, PMID:15661519, PMID:7840137]
A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell. [GOC:cilia, GOC:dgh, GOC:kmv, PMID:17009929, PMID:20144998, PMID:22118931]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998]
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. [ISBN:0813516194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides. [GOC:vw, http://en.wikipedia.org/wiki/Microtubule_organizing_center, ISBN:0815316194, PMID:17072892, PMID:17245416]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The aggregation, arrangement and bonding together of a set of components to form a non-motile cilium. [GO_REF:0000079, GOC:cilia, GOC:kmv, GOC:TermGenie, PMID:14521833, PMID:14521834]
A process in which a protein is transported to, or maintained in, a location within a ciliary membrane. [GO_REF:0000087, GOC:krc, GOC:TermGenie, PMID:22139371]
Any process that modulates the frequency of cilium beating involved in ciliary motility. [GOC:BHF, GOC:cilia, GOC:dph, GOC:krc, GOC:tb]
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2]
The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. [DOI:10.1371/journal.pone.0051070, GOC:cjm, http://www.onelook.com]
The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). [GOC:dgh, GOC:jid]
Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light. [CL:0000210, GOC:bf, GOC:rl]
The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. [CL:0000136, GOC:go_curators]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a leptin stimulus. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. It plays a key role in regulating energy intake and energy expenditure, including appetite and metabolism]. [GOC:yaf]
The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane. [ISBN:0716731363]
An increase in the internal diameter of blood vessels, especially arterioles or capillaries, due to relaxation of smooth muscle cells that line the vessels, and usually resulting in a decrease in blood pressure. [GOC:pr, ISBN:0192800981]
Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size. [GOC:dph, GOC:go_curators, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size. [GOC:dph, GOC:ems, GOC:tb]
A series of molecular signals initiated by the binding of leptin to a receptor on the surface of a cell, which reduces appetite, the desire or physical craving for food. [GOC:BHF, GOC:vk, PMID:19150989]
A process in which a protein is transported to, or maintained in, a location within an organelle. [GOC:mah]
A series of molecular signals initiated by the binding of leptin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. [GOC:mah, GOC:signaling, GOC:yaf]
Behavior in a fully developed and mature organism. [GOC:mah, ISBN:0877797099]
The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The progression of the hippocampus over time from its initial formation until its mature state. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420, UBERON:0002421]
The progression of the striatum over time from its initial formation until its mature state. The striatum is a region of the forebrain consisting of the caudate nucleus, putamen and fundus striati. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the artery. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The artery is a vessel carrying blood away from the heart. [GOC:mtg_muscle, MA:0000708, MSH:D001158]
Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process in which a protein is transported to, or maintained in, a specific location. [GOC:ai]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement. [GOC:bf, GOC:cilia, ISBN:0198547684]
Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription. [GOC:txnOH]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell. [GOC:BHF, GOC:dph, GOC:tb]
A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:signaling, ISBN:0878932437, PR:000000034]
The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:jl]
The directed movement of acetyl-CoA into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetyl-CoA is a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + H+(out) = solute(in) + H+(in). [GOC:ai]
Enables the directed movement of acetyl-CoA into, out of or within a cell, or between cells. Acetyl-CoA is a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis. [GOC:ai]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head. [GOC:dph]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell. [ISBN:0198506732]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [GOC:go_curators]
Any process that maintains the redox environment of a cell or compartment within a cell. [GOC:ai, GOC:dph, GOC:tb]
The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate. [ISBN:0198506732]
The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate. [GOC:ai]
Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. [EC:2.7.4.6]
A small amount of cytoplasm surrounded by a cell membrane that is generally retained in spermatozoa after spermiogenesis, when the majority of the cytoplasm is phagocytosed by Sertoli cells to produce \residual bodies\. Initially, the droplet is located at the neck just behind the head of an elongated spermatid. During epididymal transit, the cytoplasmic droplet migrates caudally to the annulus at the end of the midpiece; the exact position and time varies by species. The cytoplasmic droplet consists of lipids, lipoproteins, RNAs, a variety of hydrolytic enzymes, receptors, ion channels, and Golgi-derived vesicles. The droplet may be involved in regulatory volume loss (RVD) at ejaculation, and in most species, though not in humans, the cytoplasmic droplet is lost at ejaculation. Note that the cytoplasmic droplet is distinct from \excessive residual cytoplasm\ that sometimes remains in epididymal spermatozoa, particularly when spermiogenesis has been disrupted. [GOC:krc, GOC:vesicles, PMID:12672117, PMID:21076437, PMID:23159014]
The segment of the sperm flagellum where the mitochondrial sheath ends, and the outer dense fibers (ODFs) associated with outer axonemal doublets 3 and 8 are replaced by the 2 longitudinal columns of the fibrous sheath (FS) which run the length of the principal piece and are stabilized by circumferential ribs. The principal piece makes up ~2/3 of the length of the sperm flagellum and is defined by the presence of the FS and of only 7 (rather than 9) ODFs which taper and then terminate near the distal end of the principal piece. [GOC:cjm, MP:0009836]
Outer arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes. Outer dynein arms contain 2-3 heavy chains, two or more intermediate chains and a cluster of 4-8 light chains. Inner and outer dynein arms have different functions in the generation of microtubule-based motility. [GOC:BHF, GOC:vk, PMID:2557057, PMID:6218174]
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals. [GOC:mah]
Any process involved in the controlled movement of a flagellated sperm cell. [GOC:cilia, GOC:jl, GOC:krc]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. [GOC:ai]
The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2). [CHEBI:18421, GOC:jl]
The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species. [CHEBI:18421, GOC:jl]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with copper (Cu) ions. [GOC:ai]
Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide. [EC:1.15.1.1, GOC:vw, PMID:15064408]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
The controlled release of proteins from a cell. [GOC:ai]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [GOC:mah]
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. [GOC:jl, ISBN:0395825172, ISBN:0815316194]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A process in which a potassium ion is transported from one side of a membrane to the other. [GOC:mah]
The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
The intramolecular conversion of uridine to pseudouridine in a tRNA molecule. [GOC:mah]
The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. [GOC:go_curators, ISBN:1555811337]
The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs. [GOC:hjd, GOC:mah]
Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5. [EC:5.4.99.12, GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. [GOC:cilia, GOC:clt, PMID:21750193]
The portion of the photoreceptor cell cilium linking the photoreceptor inner and outer segments. It's considered to be equivalent to the ciliary transition zone. [GOC:cilia, PMID:15917207, PMID:22653444, PMID:8718680]
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. [GOC:jl, ISBN:0395825172, ISBN:0815316194]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs. [GOC:add, PMID:12019563]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of inner ear receptor cells. [GOC:dph]
The process in which relatively unspecialized cells, acquire specialized structural and/or functional features of inner ear receptor cells. Inner ear receptor cells are mechanorecptors found in the inner ear responsible for transducing signals involved in balance and sensory perception of sound. [GOC:dph]
The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion. [http://www.medterms.com, http://www.onelook.com/]
The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. [GOC:ai]
Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light. [CL:0000210, GOC:bf, GOC:rl]
The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively. [GOC:jl, ISBN:0192801023]
The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. [GOC:ai]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers. [GOC:mah, ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi  and Golgi-to-ER transport. [GOC:pr, PMID:16723730]
Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. [GOC:dph, GOC:tb]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus. [GOC:dph, GOC:jl, GOC:mah]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide. [GOC:dos, GOC:vw]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that modulates the frequency, rate or extent of osteoclast differentiation. [GOC:go_curators]
Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage. [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that modulates the frequency, rate or extent of long-term synaptic potentiation. [GOC:BHF, GOC:TermGenie]
Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task). [GOC:curators, http://www.onelook.com/, ISBN:0582227089]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
Antagonizes ribosome-mediated translation of mRNA into a polypeptide. [GOC:ai, GOC:clt]
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. [GOC:kmv, SO:0000234]
The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GOC:mah]
The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation. [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:9412464]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile. [ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [CHEBI:30413, GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. [GOC:mah]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water. [http://www.onelook.com/, ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GOC:go_curators, ISBN:0198547684]
The chemical reactions and pathways resulting in the formation of a glycosylphosphatidylinositol (GPI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The phosphatidylinositol group is linked via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via an ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GPI anchors have variants on this canonical linkage. [GOC:go_curators, ISBN:0198547684]
Catalysis of the transfer of ethanolamine phosphate to a mannose residue in the GPI lipid precursor. [PMID:15632136]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle. [ISBN:0198547684]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6. [GOC:ai]
The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y. [ISBN:0198506732]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules. [GOC:bf, GOC:dph, ISBN:0201090910, ISBN:0716720094, ISBN:0879010479, Wikipedia:Glycolysis]
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule. [GOC:mah, ISBN:0198506732]
A cellular homeostatic process involved in the maintenance of an internal steady state of glucose within a cell or between a cell and its external environment. [GOC:dph, GOC:go_curators, GOC:tb]
Catalysis of the reaction: ATP + D-mannose = ADP + D-mannose 6-phosphate. [EC:2.7.1.7]
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor). [GOC:jl]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Catalysis of the reaction: ATP + D-fructose = ADP + D-fructose 6-phosphate. [EC:2.7.1.4]
Interacting selectively and non-covalently with the D- or L-enantiomer of glucose. [CHEBI:17234, GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: ATP + D-hexose = ADP + D-hexose 6-phosphate. [EC:2.7.1.1]
Catalysis of the reaction: ATP + D-glucose = ADP + D-glucose-6-phosphate. [EC:2.7.1.2]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any process that activates or increases the frequency, rate or extent of cytotoxic T cell differentiation. [GOC:go_curators]
Any process that activates or increases the rate or extent of activated T cell proliferation. [GOC:jl]
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell.  Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. [GOC:dos, GOC:mah]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Interacting selectively and non-covalently with any member of the tumor necrosis factor receptor superfamily. [GOC:add]
Interacting selectively and non-covalently with the tumor necrosis factor receptor. [GOC:ai]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi  and Golgi-to-ER transport. [GOC:pr, PMID:16723730]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents or reduces the frequency, rate or extent of platelet-derived growth factor receptor-beta signaling pathway. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of the PERK-mediated unfolded protein response. [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22013210]
Any process that activates or increases the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway. [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, GOC:TermGenie, PMID:20160352]
Any process that stops, prevents or reduces the frequency, rate or extent of positive thymic T cell selection. [GOC:TermGenie, PMID:22080863]
Any process that stops, prevents or reduces the frequency, rate or extent of macrophage colony-stimulating factor signaling pathway. [GOC:TermGenie, PMID:16705167]
Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-4-mediated signaling pathway. [GOC:TermGenie, PMID:17210636]
Any process that stops, prevents or reduces the frequency, rate or extent of prolactin signaling pathway. [GOC:TermGenie, PMID:11773439]
Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-2-mediated signaling pathway. [GOC:TermGenie, PMID:11909529]
Any process that modulates the frequency, rate or extent of hepatocyte growth factor receptor signaling pathway. [GOC:TermGenie, PMID:18819921]
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:add, ISBN:0121245462, ISBN:0896039986]
Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-6 binding to a cell surface receptor. [GOC:BHF, GOC:mah]
Any process that decreases the rate, frequency, or extent of protein tyrosine kinase activity. [GOC:dph, GOC:tb]
Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor. [GOC:dph]
Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor. [GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of gluconeogenesis. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation. [GOC:go_curators]
Any process involved in the maintenance of an internal steady state of glucose within an organism or cell. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat6 protein. [GOC:jl, PMID:11426647]
Any process that stops, prevents, or reduces the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat5 protein. [GOC:jl, PMID:11426647]
Any process that stops, prevents, or reduces the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat1 protein. [GOC:jl, PMID:10918594]
Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity. [GOC:go_curators]
The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine. [GOC:bf]
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. [GOC:mah]
The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. [GO_REF:0000022, GOC:jid, GOC:mah, GOC:mtg_15nov05]
The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. [GO_REF:0000022, GOC:mah, GOC:mtg_15nov05]
The process of removing one or more phosphoric (ester or anhydride) residues from a molecule. [ISBN:0198506732]
Any process that decreases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development. [GOC:BHF, GOC:dph, GOC:tb]
Any process that decreases the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor. [GOC:dph, GOC:tb]
The series of molecular signals generated as a consequence of the insulin receptor binding to insulin. [GOC:ceb]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any member of the signal transducers and activators of transcription (STAT) protein family. STATs are, as the name indicates, both signal transducers and transcription factors. STATs are activated by cytokines and some growth factors and thus control important biological processes including cell growth, cell differentiation, apoptosis and immune responses. [GOC:mr, InterPro:IPR001217, PMID:21447371, PMID:24470978]
Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity. [GOC:mah]
Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse. [ISBN:0198506732]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. [EC:3.1.3, EC:3.1.3.41, GOC:curators, GOC:pg]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Interacting selectively and non-covalently with an integrin. [GOC:ceb]
Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate. [EC:3.1.3.48]
Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity. [EC:3.1.3.16, ISBN:0198547684]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
Any process that activates or increases the frequency, rate or extent of proteasomal protein catabolic process. [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:21669198]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen. [GOC:cjm, GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. [GOC:go_curators]
A prolongation or process extending from a cell, e.g. a flagellum or axon. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
An axon part that is located between the nodes of Ranvier and surrounded by compact myelin sheath. [GOC:mah, GOC:mh]
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998]
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. [ISBN:0879693568]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. [GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
The action of a molecule that contributes to the structural integrity of a cytoskeletal structure. [GOC:mah]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. [GOC:mah, GOC:pr, ISBN:0815316194]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, ISBN:0815316194]
The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. [ISBN:0815316194]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any process that activates or increases the frequency, rate or extent of cation channel activity. [GOC:BHF]
Any process that activates or increases the frequency, rate or extent of endocytic recycling. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of receptor activity. [GOC:obol]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to the cell surface. [GOC:obol]
Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription. [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw]
Any process that activates or increases the frequency, rate or extent of potassium ion transmembrane transporter activity. [GOC:BHF, GOC:TermGenie]
Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion transmembrane transporter activity. [GOC:BHF, GOC:TermGenie]
The directed movement of a protein to a specific location in the plasma membrane. [GOC:dph, GOC:tb]
An angiotensin-mediated signaling pathway where the activated receptor transmits the signal via Gq-mediated activation of phospholipase C (PLC). PLC hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) into the second messengers inositol-1,4,5,-triphosphate (IP3) and diacylglycerol (DAG). DAG activates protein kinase C (PKC), whilst IP3 binds intracellular receptors to induce the release of Ca2+ from intracellular stores. [GOC:bf, GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state. [GOC:devbiol, GOC:mtg_heart]
The removal of capping protein from the end of actin filaments to free the ends for addition, exchange or removal of further actin subunits. [GOC:pf]
The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits. [GOC:go_curators]
The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity. [GOC:jid, GOC:mah]
The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:jl]
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:jl]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
Formation of a microspike, a dynamic, actin-rich projection extending from the surface of a migrating animal cell. [ISBN:0815316194, PMID:11429692, PMID:12153987, PMID:19095735]
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. [GOC:ef, GOC:mtg_muscle, ISBN:0198506732]
Interacting selectively and non-covalently with the titin Z domain, which recognizes and binds to the C-terminal calmodulin-like domain of alpha-actinin-2 (Act-EF34), adopts a helical structure, and binds in a groove formed by the two planes between the helix pairs of Act-EF34. [GOC:mah, InterPro:IPR015129]
Interacting selectively and non-covalently with a member of the FATZ family of proteins, filamin-, actinin-, and telethonin-binding proteins of the Z-disc of striated muscle. FATZ proteins are located in the Z-disc of the sarcomere and are involved in a complex network of interactions with other Z-band components. [PMID:10984498, PMID:11699871]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient. [GOC:BHF, GOC:jl]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively. [GOC:mah, PMID:10481174]
The function of a transcription cofactor that activates transcription in conjunction with a thyroid hormone-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself. [GOC:dph, GOC:tb]
The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself. [GOC:dph, GOC:tb]
Interacting selectively and non-covalently with a LIM domain (for Lin-11 Isl-1 Mec-3) of a protein, a domain with seven conserved cysteine residues and a histidine, that binds two zinc ions and acts as an interface for protein-protein interactions. [GOC:go_curators, Pfam:PF00412]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton). [GOC:mah]
Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions. [GOC:bf, GOC:jl]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The small subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript. [GOC:curators]
The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit. [GOC:jl]
Interacting selectively and non-covalently with the small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA. [GOC:elh]
Interacting selectively and non-covalently with the 5' untranslated region of an mRNA molecule. [GOC:jid]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself. [GOC:dph, GOC:tb]
Interacting selectively and non-covalently with an estrogen receptor. [GOC:ai]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:kd, GOC:mah]
A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK). [GOC:pr, GOC:rn, PMID:7877684, PMID:9841670]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. [GOC:mah]
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. [ISBN:0198506732]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. [EC:2.7.7.7, GOC:mah]
Catalysis of the transfer of a nucleotidyl group to a reactant. [ISBN:0198506732]
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). [EC:2.7.7.31]
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group. [EC:2.7.7.7, GOC:vw, ISBN:0198547684]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Any vesicle that is part of the extracellular region. [GO_REF:0000064, GOC:pm, GOC:TermGenie, PMID:24769233]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a low-density lipoprotein particle stimulus. [GOC:mah]
A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane. [GOC:bf, GOC:mah, GOC:signaling, PMID:15006537, PMID:19643732]
Formation of the junction between an axon and the glial cell that forms the myelin sheath. Paranodal junctions form at each paranode, i.e. at the ends of the unmyelinated nodes of Ranvier. [PMID:14715942]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The binding and fusion of a sperm, having penetrated the zona pellucida, with the plasma membrane of the oocyte. Binding occurs at the posterior (post-acrosomal) region of the sperm head. [GOC:jl, http://arbl.cvmbs.colostate.edu/hbooks/pathphys/reprod/fert/fert.html]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rab family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. [GOC:go_curators]
The region of the plasma membrane located at the apical end of the cell. [GOC:curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis. [GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The directed movement of carboxylic acid across a membrane. [GO_REF:0000069, GOC:TermGenie, PMID:10869563]
The directed movement of L-ascorbic acid from one side of an epithelium to the other. [GOC:mah, GOC:yaf]
The directed movement of dehydroascorbate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dehydroascorbate, 5-(1,2-dihydroxyethyl)furan-2,3,4(5H)-trione, is an oxidized form of vitamin C. [GOC:sl]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:vw]
The process in which a vitamin is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. [GOC:bf]
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. [GOC:jid, UBERON:0002048]
The directed movement of L-ascorbic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, is vitamin C and has co-factor and anti-oxidant activities in many species. [CHEBI:38290, GOC:ai]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. [GOC:lr]
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). [GOC:dph, GOC:jid, GOC:tb, UBERON:0000955]
The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: L-ascorbate(out) + Na+(out) = L-ascorbate(in) + Na+(in). [GOC:mah, GOC:yaf, PMID:18094143]
Enables the directed movement of dehydroascorbate, 5-(1,2-dihydroxyethyl)furan-2,3,4(5H)-trione, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [CHEBI:17242]
Enables the directed movement of L-ascorbate into, out of or within a cell, or between cells. L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, is vitamin C and has co-factor and anti-oxidant activities in many species. [CHEBI:38290, ISBN:0198506732]
Enables the transfer of sodium ions (Na+) from one side of a membrane to the other. [GOC:ai, GOC:BHF]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ascorbate(out) + Na+(out) = ascorbate(in) + Na+(in). [TC:2.A.40.6.1]
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. [GOC:ai, GOC:dgf]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A structure found in the nucleolus, which contains nearly completed preribosomal particles destined for the cytoplasm. [PMID:10754561]
Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation. [GOC:dph, GOC:mah, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Any process that activates or increases the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of signal transduction. [GOC:sm]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
Interacting selectively and non-covalently with one of the p53 family of proteins. [GOC:hjd]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops or reduces the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of protein complex assembly. [GOC:mah]
A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered. [GOC:go_curators, GOC:mtg_apoptosis]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. [GOC:hjd]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport. [http://www.onelook.com]
Stops, prevents or reduces the activity of any enzyme that catalyzes the hydrolysis of ATP to ADP and orthophosphate. [GOC:jl]
A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs. [GOC:ab, GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393, PMID:18322460, PMID:19239890]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria. [GOC:mah]
Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor. [GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor signaling pathway. [GOC:add, PMID:16551253, PMID:17328678]
Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-8 production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-beta production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. [GOC:dph, GOC:rl, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of signaling in response to detection of lipopolysaccharide. [GOC:mah]
Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. [GOC:as, ISBN:0198506732]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that stops, prevents or reduces the frequency, rate or extent of peptidyl-lysine acetylation. [GOC:obol]
The modification of histone H3 by the removal of one or more acetyl groups. [GOC:BHF, GOC:rl]
The removal of an acetyl group from an acetylated lysine residue in a peptide or protein. [GOC:BHF, GOC:mah]
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor. [GOC:das, GOC:jl, ISBN:0140513590]
The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. [GOC:ai]
Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions. [GOC:mah]
Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein. [EC:3.5.1.17, RHEA:24551]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules. [GOC:bf, GOC:dph, ISBN:0201090910, ISBN:0716720094, ISBN:0879010479, Wikipedia:Glycolysis]
Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H(+). [EC:2.7.2.3, RHEA:14804]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
The process that results in the assembly of clathrin triskelia into the ordered structure known as a clathrin cage. [GOC:jid, PMID:11460887, PMID:11977118, PMID:9531549]
The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation. [ISBN:0198506732]
The series of molecular signals generated as a consequence of a dopamine receptor binding to one of its physiological ligands. [GOC:mah]
Interacting selectively and non-covalently with a clathrin light chain. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
All of the contents of a dendrite, excluding the surrounding plasma membrane. [GOC:mah]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of dendrite development. [GOC:ai]
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation). [ISBN:0198506732]
Any process that activates or increases the frequency, rate or extent of axon extension. [GOC:go_curators]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized. [GOC:dph]
The chemical reactions and pathways resulting in the breakdown of elastin. Elastin is a glycoprotein which is randomly coiled and crosslinked to form elastic fibers that are found in connective tissue. [GOC:BHF, GOC:dph, GOC:tb]
The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. [GOC:jid]
The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling. [GOC:ebc]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases angiogenesis. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The increase in size or mass of an entire multicellular organism, as opposed to cell growth. [GOC:bf, GOC:curators, GOC:dph, GOC:tb]
The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells. [GOC:cvs]
The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state. [GOC:dph, GOC:go_curators, PMID:11532397]
The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. [GOC:go_curators]
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation). [ISBN:0198506732]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine. [RESID:AA0037]
Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions are dependent on the presence of calcium ions. [GOC:mah]
Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states. [GOC:krc]
Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin. [GOC:mah, PMID:11264466]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The process in which the developmental fate of a cell becomes restricted such that it will develop into an epithelial cell. [GOC:mtg_kidney_jan10]
Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism. [GOC:bf, GOC:tb]
The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested lipids into components that may be easily absorbed and directed into metabolism. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions). [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=forebrain]
The migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The creation of greater cell numbers in the forebrain due to cell division of progenitor cells. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The directed movement of individual interneuron precursors during the embryonic development of the olfactory bulb. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The migration of cells in the cerebral cortex in which cells move orthogonally to the direction of radial migration and do not use radial glial cell processes as substrates for migration. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
The progression of the globus pallidus over time from its initial formation until its mature state. The globus pallidus is one of the basal ganglia involved with control of voluntary movement in the brain. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues. [ISBN:0878932437]
The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature. [CL:0000540, GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH]
Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter. [GOC:txnOH]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
Any process that modulates the frequency, rate or extent of NADP metabolic process. [GOC:TermGenie, PMID:23334421]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits. [GOC:ecd]
The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle. [ISBN:0198506732]
The chemical reactions and pathways involving pyruvate, 2-oxopropanoate. [GOC:go_curators]
Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. [GOC:ai]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with manganese (Mn) ions. [GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: (S)-malate + NADP+ = pyruvate + CO2 + NADPH + H+. [EC:1.1.1.40]
Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH + H+. [EC:1.1.1.38, EC:1.1.1.39]
Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate. [ISBN:0198506732]
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells. [GOC:ai, GOC:dph, GOC:tb]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes. [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html, ISBN:96235764]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate. [GOC:mah, GOC:vw, ISBN:0815316194, PMID:11242086]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. [GOC:tb]
The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung. [GOC:dph, GOC:mtg_lung]
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation. [GOC:dph, GOC:rph]
Any process that activates or increases the rate or extent of epithelial cell proliferation. [GOC:ai]
The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113]
The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus. [GOC:go_curators]
The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development. [GOC:bf, GOC:dph, GOC:jid, GOC:tb]
Any process that activates or increases the frequency, rate or extent of smoothened signaling. [GOC:go_curators]
The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively. [GOC:jl, ISBN:0192801023]
Any process that activates or increases the frequency, rate or extent of the activity of any activin receptor signaling pathway. [GOC:BHF, GOC:rl]
Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity. [GOC:dgh]
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping. [GOC:bf, GOC:jl, ISBN:0395825172]
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. [GOC:jid, UBERON:0002048]
The specification of male sex of an individual organism. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway. [GOC:dph, GOC:go_curators, GOC:tb]
The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis). [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343, ISBN:0878937420]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure. [GOC:jid]
The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands. [GOC:ceb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell.  Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. [GOC:dos, GOC:mah]
The directed movement of a protein from the cytoplasm to the nucleus. [GOC:jl]
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage. [GOC:dph]
The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells. [GOC:dph]
The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight. [GOC:jid, GOC:jl]
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. [CL:0000062, GO_REF:0000034, GOC:jid]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation. [ISBN:0815316194]
Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR). [GOC:ceb]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi  and Golgi-to-ER transport. [GOC:pr, PMID:16723730]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced. [GOC:krc, ISBN:0198506732, ISBN:0879695897]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles. [GOC:mah, ISBN:0716731363]
Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, beta-amyloid fibrils, and advanced glycation end products (AGEs). [GOC:bf, PMID:11790542, PMID:12379907, PMID:12621157, PMID:20981357]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
Self-propelled movement of a cell or organism from one location to another. [GOC:dgh]
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [ISBN:0198506732]
A series of molecular signals initiated by the sphingolipid sphingosine-1-phosphate (S1P) binding to a receptor on the surface of the cell, and which proceeds with the activated receptor transmitting the signal by promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:ascb_2009, GOC:signaling, PMID:22001186, Reactome:REACT_18416.2]
Enables the directed movement of sphingolipids into, out of or within a cell, or between cells. Sphingolipids are a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid). [GOC:ai, ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Behavior in a fully developed and mature organism. [GOC:mah, ISBN:0877797099]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The larger of the two subunits of a mitochondrial ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site). [GOC:mcc]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate). [GOC:ai]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. [EC:3.1.4, GOC:curators]
Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is increased in the presence of cGMP. [GOC:mah]
Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate. [EC:3.1.4.17]
A subcompartment of the endoplasmic reticulum consisting of tubules having membranes with high curvature in cross-section. [GOC:vw, PMID:16469703, PMID:20434336]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/]
The portion of the nuclear lumen proximal to the inner nuclear membrane. [GOC:krc, GOC:mah]
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. [GOC:mah, GOC:pz]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). [ISBN:0198547684]
The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis. [GOC:tb, GOC:vw]
The directed movement of a protein to a specific location. [GOC:bf]
The cell cycle process in which the directed movement of the mitotic spindle to a specific location in the cell occurs. [GOC:ai]
A series of molecular signals within the cell that are mediated by a member of the Ran family of proteins switching to a GTP-bound active state. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of astral microtubules, any of the spindle microtubules that radiate in all directions from the spindle poles. [GOC:mah]
The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis. [GOC:mah, ISBN:0815316194]
The cell cycle process in which the directed movement of chromosomes from the center of the spindle towards the spindle poles occurs. This mediates by the shortening of microtubules attached to the chromosomes, during mitosis. [GOC:ai]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
The directed movement of a ribosomal protein from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:ai]
The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:ai]
The directed movement of a protein from the cytoplasm to the nucleus. [GOC:jl]
A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope. [GOC:curators, ISBN:0198506732, PMID:14570049, PMID:9126736]
A protein complex assembly process that contributes to protein import into the nucleus, and that results in the association of a cargo protein, a carrier protein such as an importin alpha/beta heterodimer, and a nucleoporin located at the periphery of the nuclear pore complex. [GOC:isa_complete, GOC:mah, PMID:14570049, PMID:7878057, PMID:9126736]
Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size. [GOC:ai]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Enables the directed movement of proteins into, out of or within a cell, or between cells. [ISBN:0198506732]
Interacting selectively and non-covalently with Ran, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly. [GOC:rn, PMID:12787777, PMID:14726649]
Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus. [GOC:ai]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. [GOC:jl]
Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. [GOC:go_curators]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. [ISBN:0198506732]
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule. [GOC:mah, ISBN:0198506732]
Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. [GOC:mah, ISBN:0198506732]
Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the reaction: glycogen + phosphate = maltodextrin + alpha-D-glucose 1-phosphate. [EC:2.4.1.1, MetaCyc:GLYCOPHOSPHORYL-RXN]
Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase. [EC:2.4.1.1]
A structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus. [GOC:mtg_sensu, ISBN:0198547684]
The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. [GOC:jl]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. [http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. [GOC:go_curators]
A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters. [GOC:jl, GOC:krc, PMID:16858867, Wikipedia:Rna_polymerase_ii]
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). [ISBN:0198547684]
Any process in which the endoplasmic reticulum is maintained in a specific location within a cell and prevented from moving elsewhere. [GOC:ai, GOC:dph, GOC:tb]
The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. [ISBN:0198506732]
Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states. [GOC:krc]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a. [EC:2.7.11.19]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Catalysis of the reaction: 4 ATP + 2 phosphorylase b = 4 ADP + phosphorylase a. [EC:2.7.11.19]
A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. [GOC:bf, GOC:mah, GOC:vw, PMID:20096808, PMID:21035408]
Trimeric protein complex that possesses endonuclease activity; involved in meiotic recombination, DNA repair and checkpoint signaling. In Saccharomyces cerevisiae, the complex comprises Mre11p, Rad50p, and Xrs2p; complexes identified in other species generally contain proteins orthologous to the Saccharomyces cerevisiae proteins. [GOC:mah, GOC:vw, PMID:11988766, PMID:17674145]
A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection. [GOC:ma, PMID:10944585]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. [GOC:dph, GOC:tb]
Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. [GOC:ai]
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of DNA endoreduplication. [GOC:mah]
The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands. [GOC:isa_complete, GOC:mah]
Any process that activates or increases the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the phosphorylation by a protein of one or more of its own residues. [GOC:mah]
The formation of the single stranded telomeric 3' overhang, a conserved feature that ranges in length from 12 nt in budding yeast to approximately 500 nt in humans. [PMID:16096639]
A mitotic cell cycle checkpoint that slows DNA synthesis in response to DNA damage by the prevention of new origin firing and the stabilization of slow replication fork progression. [GOC:vw]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Synapsis begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete. [GOC:mtg_cell_cycle, PMID:22582262, PMID:23117617]
A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G2/M transition of the cell cycle in response to DNA damage. [GOC:mtg_cell_cycle]
The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other. [GOC:jh, GOC:mah, ISBN:0815316194]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear. [GOC:rph, PMID:10827453, PMID:24837021]
The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix. [GOC:elh]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with manganese (Mn) ions. [GOC:ai]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. [GOC:ai]
Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue. [ISBN:0198506732]
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end. [GOC:mah, ISBN:0198547684]
Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks. [GOC:mah, ISBN:0198547684]
Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. [GOC:mah, ISBN:0198547684]
Catalysis of the hydrolysis of ester linkages within nucleic acids. [ISBN:0198547684]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix. [EC:3.6.1.3, GOC:jl]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks. [GOC:mah]
The volume enclosed by the membranes of the endoplasmic reticulum. [ISBN:0198547684]
The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. [GOC:go_curators, NIF_Subcellular:sao-1337158144]
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. [GOC:go_curators, GOC:isa_complete]
The chemical reactions and pathways involving glycolipids, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar group acylated by one or more fatty acids and the glycerol group may be absent. [CHEBI:33563, ISBN:0198547684]
Catalysis of the transfer of a glucosyl group to an acceptor molecule, typically another carbohydrate or a lipid. [ISBN:0198506732]
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. [GOC:go_curators]
Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle. [NIF_Subcellular:sao1299635018]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. [GOC:mah, PMID:22160157]
A membrane coat adaptor complex that links clathrin to a membrane. [GOC:mah]
Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules. [GOC:mah]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. [GOC:mah]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. [GOC:ai, GOC:mah, ISBN:08789310662000]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Enables the directed movement of proteins into, out of or within a cell, or between cells. [ISBN:0198506732]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Any process that modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:mah]
The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. [GOC:as, ISBN:0198506732]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The incorporation of two iron atoms and two sulfur atoms into an iron-sulfur cluster. [GOC:jl, GOC:mengo_curators, GOC:pde, GOC:tt, GOC:vw, PMID:15952888]
The incorporation of iron into a metallo-sulfur cluster. [GOC:ai]
Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine. [EC:2.8.1.7]
Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. [GOC:mah, ISBN:0198506732]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen. [GOC:ecd, GOC:jl]
The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine). [GOC:ma]
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GOC:go_curators, ISBN:0198547684]
The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. [GOC:go_curators, ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors. [GOC:mah, ISBN:0716720094]
Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP. [EC:4.1.1.23, RHEA:11599]
Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate. [EC:2.4.2.10]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress. [GOC:ans, PMID:17284590, PMID:17601829, PMID:17967451, PMID:20368989]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing. [GOC:clt, PMID:12730603]
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway. [GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay. [GOC:mcc, GOC:TermGenie]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. [GOC:kmv, GOC:mtg_sensu, GOC:pr]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates. [CHEBI:16646, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription. [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw]
The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. [GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway. [GOC:mah]
Interacting selectively and non-covalently with a SMAD signaling protein. [GOC:ai]
Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:go_curators]
Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it. [GOC:dph, GOC:mc, GOC:nln, PMID:10218156, PMID:8409967]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
Any process that stops, prevents or reduces the frequency, rate or extent of anoikis. [GOC:obol]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. [CHEBI:33709, GOC:mah]
A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse. [GOC:dgh, GOC:dph]
The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. [GOC:bf, GOC:dph, ISBN:0815340729]
Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. [GOC:ai, GOC:pr]
Any process that modulates the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B. [GOC:ai]
The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron. [GOC:dgh]
The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. [GOC:vp, PMID:15139015]
Development of a rod cell, one of the sensory cells in the eye that reacts to the presence of light. Rod cells contain the photopigment rhodopsin or porphyropsin and are responsible for vision in dim light. [ISBN:0198506732]
Any process that modulates the rate of GTP hydrolysis by a GTPase. [GOC:jl, GOC:mah]
The process in which a relatively unspecialized cell acquires specialized features of a mechanoreceptor, a cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. [CL:0000199, GOC:jl]
A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Neurotrophins are a family of secreted growth factors that induce the survival, development, and function of neurons. [GOC:bf, GOC:jc, GOC:signaling, PMID:17466268, PR:000021998, Wikipedia:Neurotrophin]
Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine. [GOC:mah]
The series of molecular signals generated as a consequence of a brain-derived neurotrophic factor receptor binding to one of its physiological ligands. [GOC:mah]
The process in which a relatively unspecialized cell acquires specialized features of a neuron. [GOC:mah]
The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. [GOC:go_curators]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system. [GOC:ef]
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Behavior associated with the intake of food. [GOC:mah]
Any biological process in an organism that recurs with a regularity of approximately 24 hours. [GOC:bf, GOC:go_curators]
Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. [ISBN:0582227089, ISBN:0721662544]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction. [GOC:mtg_OBO2OWL_2013]
A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, GOC:signaling]
The process of introducing a phosphate group on to a protein. [GOC:hb]
The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature. [CL:0000540, GOC:go_curators]
The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes. [PMID:8999798]
Combining with a brain-derived neurotrophic factor and transmitting the signal across the plasma membrane to initiate a change in cell activity. [GOC:bf, GOC:dph]
Interacting selectively and non-covalently with brain-derived neurotrophic factor. [GOC:dgh]
Interacting selectively and non-covalently with a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth. [GOC:jl, http://www.mercksource.com/, PR:000021998]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Combining with a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth, and transmitting the signal to initiate a change in cell activity. [GOC:jl, GOC:signaling, http://www.mercksource.com/]
Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate. [EC:2.7.10.1, GOC:mah]
Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. [EC:2.7.10]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The directed, sodium-dependent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:go_curators]
Catalysis of the transfer of organic anions from one side of a membrane to the other, in a sodium dependent manner. [GOC:go_curators]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The process in which a secondary structure of RNA are broken or 'melted'. [PMID:17169986]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix. [GOC:mah, ISBN:0198506732]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
An acute behavioral change resulting from a perceived external threat. [GOC:dph, PMID:9920659]
A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. [GOC:go_curators, ISBN:0198506732]
A zone of apposition between endoplasmic-reticulum and mitochondrial membranes, structured by bridging complexes. These contact sites are thought to facilitate inter-organelle calcium and phospholipid exchange. [GOC:jl, PMID:19556461]
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. [GOC:jl, PMID:11584301]
The lipid bilayer surrounding a melanosome. [GOC:mah]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination. [GOC:vw, ISBN:0815316194]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The aggregation, arrangement and bonding together of a set of components to form a melanosome, a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. [GO_REF:0000079, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22511774]
A process that is carried out at the cellular level which results in the arrangement of constituent parts of a phagosome within a cell. Phagosome maturation begins with endocytosis and formation of the early phagosome and ends with the formation of the hybrid organelle, the phagolysosome. [GOC:kmv, GOC:tb]
A process in which a protein is transported to, or maintained in, a specific location in a membrane. [GOC:mah]
The directed movement of substances from endosomes to the melanosome, a specialised lysosome-related organelle. [PMID:16162817]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a melanosome. A melanosome is a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. [GOC:vk]
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:15771591, PMID:15928678]
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. [GOC:ai, GOC:mah, ISBN:08789310662000]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946]
Interacting selectively and non-covalently with a BLOC-2 complex, a protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. [GOC:bf, GOC:PARL, PMID:22511774]
Interacting selectively and non-covalently with the AP-3 adaptor complex. The AP-3 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of beta3, delta, mu3 and sigma3 subunits and is found associated with endosomal membranes. In at least humans, the AP-3 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (beta3A and beta3B, mu3A and mu3B, and sigma3A and sigma3B). [PMID:21097499]
Interacting selectively and non-covalently with the AP-1 adaptor complex. The AP-1 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of beta1, gamma, mu1 and sigma1 subunits and links clathrin to the membrane surface of a vesicle. In at least humans, the AP-1 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (gamma1 and gamma2, mu1A and mu1B, and sigma1A, sigma1B and sigma1C). [PMID:21097499]
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) using energy from the hydrolysis of GTP. [GOC:go_curators]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [ISBN:0198547684]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species. [GOC:go_curators, UBERON:0001003]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:hjd]
Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species. [CHEBI:38290, GOC:mah]
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. [GOC:mah]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: procollagen L-lysine + 2-oxoglutarate + O2 = procollagen 5-hydroxy-L-lysine + succinate + CO2. [EC:1.14.11.4]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane. [GOC:mtg_muscle, ISBN:0815316194]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that modulates the frequency, rate or extent of voltage-gated calcium channel activity. [GOC:BHF, GOC:TermGenie]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism. [GOC:mah]
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. [GOC:ef, GOC:mtg_muscle, ISBN:0198506732]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The small subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures. [PMID:10754561]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling. [GOC:jl]
The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52). [GOC:bf, GOC:mg2, GOC:signaling, GOC:vs, PMID:11239468, PMID:15140882]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. [GOC:dph, GOC:jl, GOC:mah]
A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate. [GOC:mtg_signal, GOC:signaling]
The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. [GOC:bf, GOC:jl, PMID:12773372, Reactome:REACT_13696.1]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the phosphorylation of the alpha or beta subunit of the inhibitor of kappaB kinase complex (IKK). [PMID:20685151]
Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [EC:2.7.11.13, GOC:bf, GOC:mah]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Any cytoplasm that is part of a axon. [GO_REF:0000064, GOC:TermGenie, PMID:18667152]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A protein complex consisting of at least tumerin and hamartin; its formation may regulate hamartin homomultimer formation. The complex acts as a GTPase activating protein (GAP) for the small GTPase (Rheb), and inhibits the TOR signaling pathway. [PMID:10585443, PMID:17121544, PMID:9580671]
The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. [GOC:nln, ISBN:0198506732]
A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter. [ISBN:0198506732, ISBN:0716731363, ISBN:0815316194]
A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. [http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The progression of an axon over time. Covers axonogenesis (de novo generation of an axon) and axon regeneration (regrowth), as well as processes pertaining to the progression of the axon over time (fasciculation and defasciculation). [GOC:dph, GOC:pg, GOC:pr]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising neurofilaments and their associated proteins. [GOC:dph]
Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors. [GOC:ai, GOC:dph, http://www.onelook.com/]
Any process that activates or increases the frequency, rate or extent of axonogenesis. [GOC:ai]
The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites. [GOC:mah]
The formation of the bundles of intermediate filaments. Intermediate filament-associated proteins (IFAPs) cross-link intermediate filaments with one another, forming a bundle or a network, and with other cell structures, including the plasma membrane. The organization of intermediate filaments and their supportive function in various cells types depends in large part on their linkage to other cell structures via IFAPs. [ISBN:0716731363]
Control of the spatial distribution of intermediate filaments; includes organizing filaments into meshworks, bundles, or other structures, as by cross-linking. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons. [GOC:go_curators, GOC:mtg_apoptosis]
Self-propelled movement of a cell or organism from one location to another. [GOC:dgh]
The assembly of neurofilaments into bundles, in which the filaments are longitudinally oriented, with numerous crossbridges between them. Neurofilament bundles may be cross-linked to each other, to membrane-bounded organelles or other cytoskeletal structures such as microtubules. [PMID:11034913, PMID:11264295]
Any process that modulates the rate, direction or extent of axon growth such that the correct diameter is attained and maintained. [GOC:dph, GOC:mah, GOC:tb]
The directed movement of mitochondria along microtubules in nerve cell axons. [GOC:ai]
The regrowth of axons outside the central nervous system (outside the brain and spinal cord) following an axonal injury. [GOC:ef]
The directed movement of organelles or molecules along microtubules from the cell periphery toward the cell body in nerve cell axons. [ISBN:0815316194]
The directed movement of organelles or molecules along microtubules from the cell body toward the cell periphery in nerve cell axons. [ISBN:0815316194]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. [GOC:mah]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. [GOC:bf, GOC:mah, GOC:vw]
Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue. [ISBN:0198506732]
The action of a molecule that contributes to the structural integrity of a cytoskeletal structure. [GOC:mah]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The small subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
A calcium channel complex in the mitochondrial inner membrane capable of highly-selective calcium channel activity. Its components include the EF-hand-containing proteins mitochondrial calcium uptake 1 (MICU1) and MICU2, the pore-forming subunit mitochondrial calcium uniporter (MCU) and its paralog MCUb, and the MCU regulator EMRE. [PMID:24231807]
An ion channel complex through which calcium ions pass. [GOC:mah]
The region between the inner and outer lipid bilayers of the mitochondrial envelope. [GOC:mah]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that decreases the concentration of calcium ions in mitochondria. [GOC:ai]
Any process that increases the concentration of calcium ions in mitochondria. [GOC:ai]
Any process involved in the maintenance of an internal steady state of calcium ions within the cytoplasm of a cell or between mitochondria and their surroundings. [GOC:ai, GOC:mah]
A process in which a calcium ion (Ca2+) is transported from one side of a membrane to the other into the mitochondrion by means of some agent such as a transporter or pore. [GOC:vw]
The directed movement of calcium ions (Ca2+) into, out of or within a mitochondrion. [GOC:ai]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. [GOC:jl]
Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. [GOC:go_curators]
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group. [ISBN:0198506732]
The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. [ISBN:0198547684]
Catalysis of the reaction: acyl-CoA + H2O = CoA + a carboxylate. [EC:3.1.2.20, MetaCyc:ACYL-COA-HYDROLASE-RXN]
Catalysis of the reaction: RCO-SR' + H2O = RCOOH + HSR'. This reaction is the hydrolysis of a thiolester bond, an ester formed from a carboxylic acid and a thiol (i.e., RCO-SR'), such as that found in acetyl-coenzyme A. [http://www.onelook.com]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The directed movement of carnitine across a membrane. [GO_REF:0000069, GOC:pr, GOC:TermGenie]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The directed movement of carnitine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carnitine is a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane. [GOC:ai]
Transport of substances into, out of or within a mitochondrion. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Enables the directed movement of carnitine across a membrane. Carnitine is a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane. [GOC:ai]
Catalysis of the reaction: carnitine (mitochondrial) + acyl carnitine (cytoplasm) = carnitine (cytoplasm) + acyl carnitine (mitochondrial). [PMID:9032458]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. [GOC:ai]
Any series of molecular signals generated as a consequence of binding to toll-like receptor 9. [GOC:add, PMID:16551253, PMID:17328678]
Any series of molecular signals generated as a consequence of binding to toll-like receptor 7. [GOC:add, PMID:16551253, PMID:17328678]
Any series of molecular signals generated as a consequence of binding to toll-like receptor 4. [GOC:add, PMID:16551253, PMID:17328678]
Any series of molecular signals generated as a consequence of binding to toll-like receptor 2. [GOC:add, PMID:16551253, PMID:17328678]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade. [GOC:ef]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with a regulatory subunit of phosphatidylinositol 3-kinase. The regulatory subunit associates with the catalytic subunit to regulate both its activity and subcellular location. [GOC:bf, PMID:20505341]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). [GOC:go_curators]
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GOC:go_curators, ISBN:0198547684]
The chemical reactions and pathways resulting in the breakdown of arginine, 2-amino-5-(carbamimidamido)pentanoic acid. [CHEBI:29016, GOC:go_curators]
Catalysis of the reaction: 4-fumarylacetoacetate + H(2)O = acetoacetate + fumarate + H(+). [EC:3.7.1.2, RHEA:10247]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends. [GOC:mah, PMID:17072889, PMID:17938628]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. [GOC:dph, GOC:tb]
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication. [GOC:vw, PMID:16464006, PMID:22064477]
The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). [GOC:add, ISBN:0781700221, ISBN:0781735149]
A process that prevents non-homologous end joining at telomere, thereby ensuring that telomeres do not fuse. [GOC:mah]
The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. [GO_REF:0000022, GOC:mah, GOC:mtg_15nov05]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. [PMID:12509526]