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 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 sodium 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 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]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The process in which 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 neuron. [GOC:dph, GOC:isa_complete, GOC:tb]
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]
Any process that maintains the redox environment of a cell or compartment within a cell. [GOC:ai, GOC:dph, GOC:tb]
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]
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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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 chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester. [ISBN:0198547684]
Catalysis of the reaction: CTP + (R)-4'-phosphopantothenate + L-cysteine = CMP + diphosphate + (R)-4'-phosphopantothenoyl-L-cysteine. Cysteine can be replaced by some of its derivatives. [EC:6.3.2.5]
An adherens junction which connects a cell to another cell. [GOC:hb]
Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils. [ISBN:0815316194]
Any process that activates or increases the frequency, rate or extent of mitotic cell cycle phase transition. [GOC:mtg_cell_cycle, GOC:TermGenie, PMID:22841721]
The attachment of one cell to another cell via adhesion molecules. [GOC:dos]
The binding of a protein or protein complex to the pointed (or minus) end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits. [ISBN:071673706X]
The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure. [GOC:devbiol]
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]
Any cadherin binding that occurs as part of the process of cell-cell adhesion. [GOC:dos]
Interacting selectively and non-covalently with tropomyosin, a protein associated with actin filaments both in cytoplasm and, in association with troponin, in the thin filament of striated muscle. [GOC:curators, 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 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 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]
Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of Ras protein signal transduction. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation. [GOC:go_curators]
The process of T cell selection that occurs in the thymus. [ISBN:0781735149, PMID:12414722]
The process of sparing immature T cells in the thymus which react with self-MHC protein complexes with low affinity levels from apoptotic death. [ISBN:0781735149, PMID:12414722]
The multiplication or reproduction of common myeloid progenitor cells, resulting in the expansion of a cell population. A common myeloid progenitor cell is a progenitor cell committed to the myeloid lineage. [CL:0000049, GOC:BHF]
Any process that stops, prevents, or reduces the frequency, rate, or extent of neutrophil apoptotic process. [GOC:add, GOC:mtg_apoptosis]
The chemical reactions and pathways involving myo-inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with three phosphate groups attached. [CHEBI:24540, CHEBI:24848, 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 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]
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 process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. [CL:0000763, GOC:add]
Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. [GOC:hjd]
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]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H(+). [EC:2.7.1.127, RHEA:11023]
A subcomplex of the nuclear pore complex (NPC) that forms the inner rings of the core scaffold, a lattice-like structure that gives the NPC its shape and strength. In S. cerevisiae, the two inner rings are each composed of Nup192p, Nup188p, Nup170p and Nup157p. In vertebrates, the two inner rings are each composed of Nup205, Nup188 and Nup155. Components are arranged in 8-fold symmetrical 'spokes' around the central transport channel. A single 'spoke', can be isolated and is sometimes referred to as the Nup170 complex. [GOC:dgf, PMID:18046406, PMID:19524430, PMID:20947011, PMID:22419078]
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]
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. [ISBN:0198547684]
The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex. [GOC:ai, 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 nuclear pore. [GOC:dph, GOC:jid, GOC:jl, GOC:mah]
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]
The action of a molecule that contributes to the structural integrity of the nuclear pore complex. [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 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 region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. [GOC:cjm, GOC:elh, GOC:kmv, GOC:pr]
A protein complex that has protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic, scaffolding, and regulatory subunits. The catalytic and scaffolding subunits form the core enzyme, and the holoenzyme also includes the regulatory subunit. [GOC:mah, ISBN:0198547684, PMID:17245430]
Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand. [GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation. [GO_REF:0000058, GOC:jz, GOC:TermGenie, PMID:25212395]
The removal of phosphoric residues from peptidyl-O-phospho-L-serine to form peptidyl-serine. [GOC:bf]
The cell cycle process in which centromeres of sister chromatids are joined during meiosis. [PMID:14730319, PMID:16325576]
The process in which sister chromatids are physically detached from each other during mitosis. [GOC:ai]
The lengthening of the distance between poles of the spindle during a meiotic cell cycle. [GOC:ai]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. [GOC:dph, GOC:ems, GOC:mah, GOC:vw]
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
The aggregation, arrangement and bonding together of a set of components to form a protein complex. [GOC:ai]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Modulates the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule. [GOC:ai]
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. [GOC:jl, ISBN:0198506732, ISBN:0721662544]
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]
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 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]
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]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
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 direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised. [PMID:9635420]
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. [GOC:BHF, GOC:dph, 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]
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 modulates the frequency, rate or extent of RNA splicing, the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GOC:jl]
The process of introducing a phosphate group on to a protein. [GOC:hb]
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]
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]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
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]
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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum. [GOC:mah]
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 stops, prevents, or reduces 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]
The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine. [RESID:AA0037]
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
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]
Any process that modulates the frequency, rate or extent of chromatin assembly or disassembly. [GOC:go_curators]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The process in which paired chromosomes are physically detached from each other during male meiosis. [GOC:ai]
Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction. [GOC:dph, ISBN:0198506732]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
The first meiotic nuclear division in which homologous chromosomes are paired and segregated from each other, producing two haploid daughter nuclei. [GOC:dph, GOC:jl, GOC:mtg_cell_cycle, PMID:9334324]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
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]
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]
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 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]
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 covalent or noncovalent attachment of a chromophore to a protein. [GOC:ma]
The series of molecular signals generated as a consequence of excitation of rhodopsin by a photon and the events that convert the absorbed photons into a cellular response. [GOC:bf, GOC:dph, GOC:hb, GOC:signaling, GOC:tb]
The sequence of reactions within a cell required to convert absorbed photons into a molecular signal. [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]
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 function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation. [GOC:ai, GOC:go_curators]
Combining with incidental electromagnetic radiation, particularly visible light, 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, GOC:dph, ISBN:0198506732]
Interacting selectively and non-covalently with 11-cis retinal, an isomer of retinal that plays an important role in the visual process in most vertebrates. 11-cis retinal combines with opsin in the rods (scotopsin) to form rhodopsin or visual purple. Retinal is one of the three compounds that makes up vitamin A. [CHEBI:16066]
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 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]
Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G-protein coupled receptors to an effector protein. [ISBN:0198547684]
The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process. [GOC:ai, http://www.onelook.com/]
The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent increase in the concentration of inositol trisphosphate (IP3) and diacylglycerol (DAG). [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 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 a G-protein beta subunit. [GOC:mah]
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]
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 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]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
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]
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]
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 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 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 nervous tissue over time, from its formation to its mature state. [GOC:dgh]
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 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 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 endothelial cell apoptotic process. [GOC:BHF, GOC:mah, GOC:mtg_apoptosis]
Any process that increases the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments. [GOC:ascb_2009, GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:mah]
Any process that activates, maintains or increases the frequency, rate or extent of the change in the membrane potential of the mitochondria from negative to positive. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme. [GOC:ai]
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 series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, GOC:signaling, PR:000001971]
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 angiogenesis. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade. [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]
A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a VEGFR on the surface of a cell, which activates or increases the frequency, rate or extent of endothelial cell chemotaxis. [GOC:bf, GOC:BHF, GOC:rl, PMID:21245381]
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 vascular endothelial growth factor stimulus. [GOC:BHF, GOC:rl, PMID:18440775]
A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response. [GOC:bf, GOC:BHF, PMID:20192754]
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, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation. [GOC:go_curators, PMID:9412464]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade. [GOC:ef]
Any process that increases 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 modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
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 activates or increases the rate or extent of endothelial cell proliferation. [GOC:add]
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 any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate. [GOC:curators]
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 an integrin. [GOC:ceb]
Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity. [GOC:mah, GOC:signaling]
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]
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]
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]
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 RNA interference. [GOC:kmv, GOC:TermGenie, PMID:22412382]
Transport of pre-microRNAs (pre-miRNAs) from the nucleus to the cytoplasm. Pre-miRNAs are a ~60-70 nucleotide stem loop intermediate in miRNA production, produced by the nuclear cleavage of a primary miRNA (pri-mRNA) transcript. Pre-miRNAs are transported from the nucleus to the cytoplasm where further cleavage occurs to produce a mature miRNA product. [GOC:sl, PMID:14744438]
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 protein from the nucleus into the cytoplasm. [GOC:jl]
Enables the directed movement of pre-miRNAs between the nucleus and the cytoplasm of a cell. [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:14681208]
Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA. [PMID:18951094]
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 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]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with transfer RNA. [GOC:ai]
The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex. [GOC:mtg_sensu, 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]
The aggregation, arrangement and bonding together of a mature, active proteasome regulatory particle complex. [GOC:mah, GOC:rb, PMID:19412159]
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 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 process leading to the attainment of the full functional capacity of a protein. [GOC:ai]
The removal of sugar residues from a glycosylated protein. [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 reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H(2)O = N-acetyl-beta-D-glucosaminylamine + L-aspartate + H(+). [EC:3.5.1.26, RHEA:11547]
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 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 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 process of directing proteins towards the lysosome using signals contained within the protein. [GOC:curators]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Enables the directed movement of proteins into, out of or within a cell, or between cells. [ISBN:0198506732]
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]
Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol. [ISBN:0198506732]
A ribonucleoprotein complex that contains small nuclear RNA U2. [GOC:krc, GOC:mah]
Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends. [GOC:krc, GOC:mah, PMID:11343900]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
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 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]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
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 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 process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure. [GOC:jid]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_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]
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 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 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 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]
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]
A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome. [GOC:clt, ISBN:0815316194]
Any process that modulates the frequency, rate or extent of the separation of duplicated centrosome components at the beginning of mitosis. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [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 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]
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]
The chemical reactions and pathways resulting in the formation of 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]
The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester. [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 phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids. [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]
Any process that activates or increases the frequency, rate or extent of production of a cytokine. [GOC:add, ISBN:0781735149]
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 transfer of an acyl group to an oxygen atom on the acylglycerol molecule. [GOC:ai]
Catalysis of the reaction: acyl-CoA + 1-acyl-sn-glycerol-3-phosphate = CoA + 1,2-diacyl-sn-glycerol-3-phosphate. [EC:2.3.1.51, GOC:ab]
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 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]
Catalysis of the hydrolysis of any O-glycosyl bond. [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 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 actin and associated proteins. Includes actin cytoskeleton-associated complexes. [GOC:jl, ISBN:0395825172, 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 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]
Any process that increases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. [GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells. [GOC:jid]
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 protein kinase activity. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of osteoblast differentiation. [GOC:go_curators]
A series of molecular signals initiated by the binding of collagen to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:uh, PMID:15888913, PMID:16626936]
The multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage. [CL:0000138, GOC:yaf, PMID:21484705]
Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation. [PMID:15132736]
Any process that modulates the frequency, rate or extent of bone mineralization. [GOC:go_curators]
Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix. [GOC:mah, ISBN:0815316194]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
Any process that increases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium. [GOC:BHF, GOC:dph, GOC:tb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
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 increase in size or mass of an endochondral bone that contributes to the shaping of the bone. [GOC:ascb_2009, GOC:dph, GOC:tb]
Combining with collagen 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. [GOC:bf, GOC:uh, PMID:16626936, PMID:21568710]
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 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]
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]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
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 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 superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion. [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]
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 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 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]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
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]
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 frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [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]
Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds. [GOC:jl]
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]
Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides. [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 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 cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
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 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]
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 modulates the frequency, rate or extent of cellular DNA-templated transcription. [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 a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with beta-amyloid peptide/protein and/or its precursor. [GOC:hjd]
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]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A pentameric complex that includes orthologues of human PIR121, Nap1, Abi, SCAR, and HSPC300 and regulates actin polymerization and/or depolymerization through small GTPase mediated signal transduction. [GOC:hla, GOC:pg, PMID:12181570, PMID:24036345, PMID:24630101]
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]
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]
Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA. [GOC:jid]
Any process that activates or increases the frequency, rate or extent of Arp2/3 complex-mediated actin nucleation. [PMID:21454476]
Long distance growth of a single dendrite involved in cellular development. [GOC:BHF, GOC:rl]
Any process that activates or increases the frequency, rate or extent of the neurotrophin TRK receptor signaling pathway. [GOC:ai]
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]
Long distance growth of a single axon process involved in cellular development. [GOC:BHF, GOC:dgh, GOC:dph, GOC:jid, GOC:lm, GOC:rl]
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]
Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell. [GOC:mah, ISBN:0815316194]
A series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state. [GOC:bf]
Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases. [GOC:ebc, PMID:11702775]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
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 that modulates the frequency, rate or extent of the attachment of spindle microtubules to the kinetochore. [GOC:ai]
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart. [GOC:go_curators, GOC:mah]
A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules. [GOC:mah, GOC:vw, PMID:11408572, PMID:18367542, PMID:8027178]
The growing (plus) end of a microtubule. In vitro, microtubules polymerize more quickly at the plus end than at the minus end. In vivo, microtubule growth occurs only at the plus end, and the plus end switches between periods of growth and shortening, a behavior known as dynamic instability. [GOC:bf, GOC:lb, PMID:12700769, PMID:16643273]
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 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]
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]
Methylation of the ribose of the first nucleotide of a 5'-capped mRNA. [GOC:sp, PMID:20713356]
The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule. [PMID:18505803]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript. [GOC:mah, PMID:9266685]
Catalysis of the transfer of a methyl group to an acceptor molecule. [ISBN:0198506732]
Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine. [EC:2.1.1.57]
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]
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 a very-low-density lipoprotein particle and delivering the very-low-density lipoprotein into the cell via endocytosis. [GOC:bf, ISBN:0198506732]
Interacting selectively and non-covalently with calcium ions (Ca2+). [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]
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 activates or increases the frequency, rate or extent of dendrite development. [GOC:TermGenie]
The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell. [GOC:jl, ISBN:0198506732]
Any process that activates or increases the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
A series of molecular signals initiated by the binding of reelin (a secreted glycoprotein) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, PMID:12827279, PMID:20223215, PR:000013879]
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 directed movement of a glycoprotein, any protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:BHF, GOC:mah, GOC:rl]
The process whose specific outcome is the progression of the ventral region of the spinal cord over time, from its formation to the mature structure. The neurons of the ventral region of the mature spinal cord participate in motor output. [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 transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
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]
Combining with the secreted glycoprotein reelin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:bf, PMID:12827279, PMID:20223215, PR:000013879]
Enables the directed movement of a glycoprotein, any protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells. [GOC:BHF, GOC:mah, GOC:rl]
Interacting selectively and non-covalently with a very-low-density lipoprotein particle, 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. [GOC:BHF, GOC:mah]
Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex. [GOC:BHF, GOC:rl]
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]
The lipid bilayer surrounding a recycling endosome. [GOC:jid, GOC:rph, PMID:10930469, PMID:15601896, PMID:16246101]
The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network. [GOC:mah]
A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25. [GOC:bhm, GOC:pr, PMID:10872468, PMID:19450911]
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 lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
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 calcium ion-dependent exocytosis. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. [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 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 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 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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the reaction: acetyl-CoA + glyoxylate + H(2)O = (S)-malate + CoA + H(+). [EC:2.3.3.9, RHEA:18184]
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 magnesium (Mg) ions. [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 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]
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]
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]
A cellular membrane associated with the pre-autophagosomal structure. [GOC:mah, GOC:rph, PMID:16874040, PMID:17382324]
The lipid bilayer surrounding an endosome. [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 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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered. [GOC:autophagy, GOC:isa_complete]
A punctate structure localized in the vicinity of the vacuole that is required for the formation of autophagosomes. [GOC:elh, PMID:11689437, PMID:12048214, PMID:12554655]
The process in which vesicles are directed to specific destination membranes during transport from the trans-Golgi to the endosome. [GOC:jid, GOC:mah, ISBN:0716731363, PMID:10219233]
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]
Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions. [GOC:bf, PMID:18397324]
Interacting selectively and non-covalently with an androgen receptor. [GOC:ai]
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 an estrogen 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]
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]
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 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 biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities. [GOC:dph, ISBN:0721662544]
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 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 stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. [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 in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping. [UBERON:0002101]
Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of bone mineralization. [GOC:go_curators]
The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue. [GOC:mah, PMID:22936354]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/]
Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein. [EC:2.7.10.2]
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 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 of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer. [GOC:ai]
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 metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway. [http://www.peroxisome.org/Scientist/Biochemistry/alpha-oxidation.html]
Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate. [ISBN:0198506732]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases. [CHEBI:45931, GOC:mlg]
Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. [GOC:jl]
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]
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]
Interacting selectively and non-covalently with magnesium (Mg) ions. [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]
Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. [GOC:mah, NIF_Subcellular:sao1045389829]
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]
Reactions triggered in response to the presence of a virus that act to protect the cell or organism. [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]
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 outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope. [GOC:ai]
Any process that modulates the frequency, rate or extent of peroxisome organization. [GOC:TermGenie, PMID:7500953]
Any process that activates or increases the frequency, rate, or extent of production of IP-10. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of production of chemokine (C-C motif) ligand 5. [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 exogenous double-stranded RNA stimulus. [GOC:mah]
Any process that increases 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 activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription. [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]
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 stops, prevents, or reduces the frequency, rate or extent of viral genome replication. [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 the movement of a transcription factor from the cytoplasm to the nucleus. [GOC:jl]
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. [GOC:jl]
Any series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA. RIG-I detects RNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines. [GOC:bf, PMID:17328678, PMID:19620789, PMID:21435580]
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 tumor necrosis factor production. [GOC:mah]
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 interferon-beta production. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of interferon-alpha production. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. [GOC:add, 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 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 process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, GOC:mtg_sensu, ISBN:0781735149, PMID:15199967, PMID:16177805]
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 CARD (N-terminal caspase recruitment) domain, a protein-protein interaction domain that belongs to the death domain-fold superfamily. These protein molecule families are similar in structure with each consisting of six or seven anti-parallel alpha-helices that form highly specific homophilic interactions between signaling partners. CARD exists in the N-terminal prodomains of several caspases and in apoptosis-regulatory proteins and mediates the assembly of CARD-containing proteins that participate in activation or suppression of CARD carrying members of the caspase family. [PMID:12054670]
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 chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. [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]
Catalysis of the reaction: acetoacetyl-CoA + acetyl-CoA + H(2)O = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA + H(+). [EC:2.3.3.10, RHEA:10191]
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 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 cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis. [GOC:ma]
The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine. [RESID:AA0076]
The methylation of peptidyl-lysine to form peptidyl-N6,N6,N6-trimethyl-L-lysine. [RESID:AA0074]
Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate. [PMID:12054878]
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]
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]
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]
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 metalloendopeptidase activity. [GO_REF:0000059, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:18591254]
Any process that activates or increases the frequency, rate or extent of TRAIL-activated apoptotic signaling pathway. [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24939851]
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]
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 frequency, rate or extent of membrane protein ectodomain proteolysis. [GOC:ai]
Any process that stops or reduces the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
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 organic substance stimulus. [GOC:sm]
Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity. [GOC:ai]
Interacting selectively and non-covalently with any protease or peptidase. [GOC:hjd]
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 vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
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]
The lipid bilayer surrounding a cytoplasmic vesicle. [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]
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 activity of a GTPase. [GOC:jl, GOC:mah]
Generation of the cleavage furrow, a shallow groove in the cell surface near the old metaphase plate that marks the site of cytokinesis. This process includes the recruitment and localized activation of signals such as RhoA at the site of the future furrow to ensure that furrowing initiates at the correct site in the cell. [GOC:ans, PMID:15811947, PMID:20687468, PMID:2192590]
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 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]
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. [GOC:dph, GOC:ma, GOC:mah, ISBN:0198547684]
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]
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 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-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 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]
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 chloride across a membrane. [GOC:TermGenie, GOC:vw]
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 ethanol 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 zinc ion 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 amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. [CHEBI:33709, GOC:mah]
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]
The process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. [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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. [CHEBI:33709, GOC:ef, GOC:mlg]
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 series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:krc]
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 transmembrane transfer of a chloride ion by a channel that opens when glycine has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Enables the transmembrane transfer of an ion by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Enables the transmembrane transfer of a chloride ion by a channel that opens when extracellular glycine has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Interacting selectively and non-covalently with glycine, aminoethanoic acid. [GOC:ai]
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]
A heterodimeric protein complex consisting of conserved large and small U2AF subunits that contributes to spliceosomal RNA splicing by binding to consensus sequences at the 3' splice site. U2AF is required to stabilize the association of the U2 snRNP with the branch point. [GOC:dos, GOC:mah, PMID:15231733, PMID:1538748, PMID:2963698, PMID:8657565]
A spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation. [GOC:ab, GOC:krc, GOC:mah, PMID:17332742, 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/]
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]
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 consisting of Prp19 and associated proteins that is involved in the transition from the precatalytic spliceosome to the activated form that catalyzes step 1 of splicing, and which remains associated with the spliceosome through the second catalytic step. It is widely conserved, found in both yeast and mammals, though the exact composition varies. In S. cerevisiae, it contains Prp19p, Ntc20p, Snt309p, Isy1p, Syf2p, Cwc2p, Prp46p, Clf1p, Cef1p, and Syf1p. [GOC:krc, PMID:16540691, PMID:19239890]
A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript. [GOC:krc, ISBN:0879695897, PMID:9150140]
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 modulates the frequency, rate or extent of mitochondrion degradation (mitophagy). [GO_REF:0000058, GOC:autophagy, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24600391]
Any process that stops, prevents or reduces the rate or extent of mRNA splicing via a spliceosomal mechanism. [GOC:jid]
Any process that activates or increases the frequency, rate or extent of RNA splicing. [GOC:mah]
The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GOC:krc, GOC:mah]
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide. [GOC:mah]
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 a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion. [GOC:BHF, GOC:mah, Pfam:PF00096]
Interacting selectively and non-covalently with the pre-mRNA 3' splice site sequence. [GOC:jl]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Interacting selectively and non-covalently with any stretch of pyrimidines (cytosine or uracil) in an RNA molecule. [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]
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 signal transduction mediated by the JNK cascade. [GOC:bf]
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 JUN kinase activity. [GOC:jl]
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]
The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine. [RESID:AA0038]
The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine. [RESID:AA0037]
The initiation of the activity of the inactive enzyme JUN kinase (JNK). [GOC:bf]
The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress. [GOC:bf, PMID:11790549]
A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened. [GOC:mah, PMID:15205520]
The process of introducing a phosphate group on to a protein. [GOC:hb]
The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK). [PMID:9561267]
Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways. [PMID:9144210]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the phosphorylation and activation of a MAP kinase kinase; each MAP kinase kinase can be phosphorylated by any of several MAP kinase kinase kinases. [PMID:9561267]
Catalysis of the reaction: JNKK + ATP = JNKK phosphate + ADP. This reaction is the phosphorylation and activation of JUN kinase kinases (JNKKs). [GOC:bf]
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 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]
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]
The chemical reactions and pathways resulting in the formation of testosterone, an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4 C-5. [GOC:dph, GOC:yaf]
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 progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants. [GOC:jl, http://www.cogsci.princeton.edu/]
The process whose specific outcome is the progression of the female genitalia over time, from formation to the mature structure. [GOC:mah]
The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure. [GOC:ems, ISBN:0140512888]
The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure. [GOC:jid]
The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics. [ISBN:0198506732]
The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. [ISBN:0198547684]
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 chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification. [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]
Catalysis of the reaction: testosterone + NAD(P)+ = androst-4-ene-3,17-dione + NAD(P)H + H+. [EC:1.1.1.51]
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 the removal of a C-5 double bond in the B ring of a sterol. [ISBN:0943088399]
Catalysis of the reaction: a 3-oxo-5-alpha-steroid + acceptor = a 3-oxo-delta(4)-steroid + reduced acceptor. [EC:1.3.99.5]
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 organic hydroxy compound. [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]
The chemical reactions and pathways involving progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants. [GOC:jl, http://www.cogsci.princeton.edu/]
The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. [CHEBI:24621, GOC:jl]
The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. [ISBN:0198547684]
Catalysis of the reaction: testosterone + donor-H2 + O2 = 6-beta-hydroxytestosterone + H2O. [GOC:ai, PMID:11726664]
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]
Catalysis of the formation of a hydroxyl group on a steroid by incorporation of oxygen from O2. [ISBN:0721662544]
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]
RNA polymerase I, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces rRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase III and others of which are also found in RNA polymerases II and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template. [GOC:krc, GOC:mtg_sensu]
RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template. [GOC:krc, GOC:mtg_sensu]
RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template. [GOC:krc, GOC:mtg_sensu]
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 synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter. [GOC:jl, 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]
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [EC:2.7.7.6, GOC:pf]
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 reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [GOC:txnOH]
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [GOC:txnOH]
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [GOC:txnOH]
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 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 the chemical reactions and pathways resulting in the formation of MHC class II. [GOC:go_curators]
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 zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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]
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 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]
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]
The series of events by which a mechanical stimulus is received and converted into a molecular signal. [GOC:ai, GOC:dos]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. [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]
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]
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 region of the plasma membrane located at the apical end of the cell. [GOC:curators]
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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
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 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]
Any process that activates or increases the frequency, rate or extent of stem cell proliferation. [GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell-cell adhesion mediated by cadherin. [GOC:obol]
The attachment of one cell to another cell via adhesion molecules. [GOC:dos]
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 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 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]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure. [GOC:go_curators]
Any cadherin binding that occurs as part of the process of cell-cell adhesion. [GOC:dos]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
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 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 intrinsic apoptotic signaling pathway in response to DNA damage. [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, GOC:TermGenie, PMID:15314165]
Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors. [GOC:TermGenie, PMID:17245429]
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]
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]
A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:BHF, GOC:mah, GOC:signaling]
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]
The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus. [GOC:add, PMID:15826826, PMID:16319493, PMID:16551252, PMID:16551262]
The initial formation of a blastocyst from a solid ball of cells known as a morula. [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]
Interacting selectively and non-covalently with a SMAD signaling protein. [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]
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 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 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 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, 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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. [EC:6, GOC:mah]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [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]
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 large subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. [GOC:hjd]
Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-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 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]
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 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 modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. [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 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 a dipeptide. [http://www.onelook.com]
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 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 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 proteasome found in the nucleus of a cell. [GOC:mah]
A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex. [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 subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex. [GOC:rb]
A multisubunit complex, which caps one or both ends of the proteasome core complex. This complex recognizes and unfolds ubiquitinated proteins, and translocates them to the proteasome core complex. [GOC:mtg_sensu, GOC:rb]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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 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 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 sucrose into, out of or within a cell, or between cells by means of some agent such as a transporter or pore. Sucrose is the disaccharide fructofuranosyl-glucopyranoside. [GOC:ai]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sucrose(out) + H+(out) = sucrose(in) + H+(in). [TC:2.A.1.5.3]
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 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 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 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 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 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 multiplication or reproduction of fibroblast cells. [GOC:jid]
The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules. [GOC:add, ISBN:0781735149, PMID:15771591]
The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein. [GOC:add, ISBN:0781735149, PMID:15771591]
Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. [GOC:ai]
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 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 by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules. [GOC:yaf, PMID:1825999, UniPathway:UPA00193]
The chemical reactions and pathways resulting in the formation of folic acid and its derivatives. [GOC:ai]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the reaction: 5-formyltetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + H(+) + phosphate. [EC:6.3.3.2, RHEA:10491]
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 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]
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]
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]
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 region of a mitochondrion to which the DNA is confined. [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]
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]
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 ammonia stimulus. [GO_REF:0000071, GOC:TermGenie, PMID:23509267]
The chemical reactions and pathways resulting in the formation of carbamoyl phosphate, an intermediate in the urea cycle and other nitrogen compound metabolic pathways. [CHEBI:17672, GOC:mah, GOC:rph]
The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine. [ISBN:0198506732]
The chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water. [GOC:ai]
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 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 chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol. [ISBN:0198506732]
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium. [CHEBI:51143, GOC:go_curators, GOC:jl, ISBN:0198506732]
The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid. [GOC:ai]
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]
Interacting selectively and non-covalently with a modified amino acid. [CHEBI:83821, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: 2 ATP + L-glutamine + CO2 + H2O = 2 ADP + phosphate + glutamate + carbamoyl phosphate. [EC:6.3.5.5]
Catalysis of the reaction: 2 ATP + CO(2) + H(2)O + NH(4)(+) = 2 ADP + carbamoyl phosphate + 5 H(+) + phosphate. [EC:6.3.4.16, RHEA:10627]
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 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 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 chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate 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]
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]
Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer. [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 reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the si-face of oxaloacetate; acetyl-CoA thus provides the two carbon atoms of the pro-S carboxymethyl group. [EC:2.3.3.1, ISBN:0121227073]
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]
Any process that activates or increases the frequency, rate or extent of signal transduction. [GOC:sm]
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]
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 component of the endoplasmic reticulum 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:curators, GOC:dos]
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]
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]
The volume enclosed by the membranes of the endoplasmic reticulum. [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 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]
Any process that modulates the frequency, rate or extent of protein localization to the cell surface. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of synaptic vesicle endocytosis. [GOC:BHF, GOC:TermGenie]
The directed movement of proteins into, out of or within a cell, or between cells, mediated by chaperone molecules that bind to the transported proteins. [GOC:mah, PMID:20378773]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane. [GOC:mah]
The chemical reactions and pathways resulting in the breakdown of misfolded proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation. [GOC:mah, GOC:vw, PMID:14607247, PMID:19520858]
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]
Any process that modulates the frequency, rate or extent of the directed movement of the catecholamine neurotransmitter dopamine into a cell. [GOC:ai]
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]
The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release. [GOC:rb]
The directed movement of synaptic vesicles. [GOC:jid, GOC:lmg, 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 intermediate filaments and their associated proteins. [GOC:ai]
The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface. [GOC:jl]
A process in which a protein is transported to, or maintained in, a location within the nucleus. [GOC:ecd]
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 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 the nuclear envelope. [GOC:dph, GOC:ems, GOC:jl, GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. [GOC:mah]
The removal of a ubiquitin-like protein of the NEDD8 type from a protein. [GOC:krc]
Interacting selectively and non-covalently with a misfolded protein. [GOC:ai]
Interacting selectively and non-covalently with an unfolded protein. [GOC:ai]
Interacting selectively and non-covalently and stoichiometrically with kinesin, a member of a superfamily of microtubule-based motor proteins that perform force-generating tasks such as organelle transport and chromosome segregation. [GOC:curators, PMID:8606779]
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 any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton). [GOC:mah]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [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]
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]
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 a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
Interacting selectively and non-covalently with the mismatch repair complex MutSalpha. [GOC:vk]
Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site. [GOC:elh, PMID:11554296]
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 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]
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 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 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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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 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]
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]
The process in which a secondary structure of RNA are broken or 'melted'. [PMID:17169986]
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 process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GOC:krc, GOC:mah]
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. [GOC:curators]
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 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 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 composed of the Fanconi anaemia (FA) proteins including A, C, E, G and F (FANCA-F). Functions in the activation of the downstream protein FANCD2 by monoubiquitylation, and is essential for protection against chromosome breakage. [GOC:jl, PMID:12093742]
A protein complex involved in regulation of mRNA processing and apoptosis. It binds to RNA in a sequence-independent manner and is recruited to the EJC prior to or during the splicing process. In humans the core proteins are RNPS1, SAP18 and ACIN1. [GOC:dph, PMID:12665594, PMID:16314458, PMID:22388736]
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]
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]
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 monocyte differentiation. [GOC:go_curators]
The compaction of chromatin during apoptosis. [GOC:mah]
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. [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 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 protein complex that contains TRIP4 (ASC1) and acts a transcriptional coactivator by interacting with transcription factors such as NF-kappa B.  In humans this complex has 4 subunits: TRIP4 + ASCC1-3. [PMID:12077347]
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 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 interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands. [GOC:isa_complete, GOC:mah]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT). [PMID:10946226]
Catalysis of the reaction: ATP + H2O = ADP + phosphate; drives the unwinding of the DNA helix in the direction 3' to 5'. [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 an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
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:mah, ISBN:071673706X]
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 process in which an anion 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]
Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [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]
Enables the transmembrane transfer of an anion by a volume-sensitive channel. An anion is a negatively charged ion. A volume-sensitive channel is a channel that responds to changes in the volume of a cell. [GOC:dph, 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]
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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
The binding of a cell to the extracellular matrix via adhesion molecules. [GOC:hb]
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]
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 multiplication or reproduction of cells, resulting in the expansion of a condensed mesenchymal cell population. A condensed mesenchymal cell population is a population of adherent mesenchymal cells. [GOC:mtg_kidney_jan10]
The process whose specific outcome is the progression of the nephron over time, from its formation to the mature structure. A nephron is the functional unit of the kidney. [GOC:mtg_kidney_jan10]
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 proteasome complex found in the cytosol of a cell. [GOC:mah, GOC:mtg_sensu]
A proteasome found in the nucleus of a cell. [GOC:mah]
A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex. [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 subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex. [GOC:mtg_sensu, GOC:rb]
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 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 activates or increases the frequency, rate or extent of proteasomal protein catabolic process. [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:21669198]
Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation. This process acts on misfolded proteins as well as in the regulated degradation of correctly folded proteins. [GOC:mah, GOC:rb, PMID:14607247, PMID:19520858]
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 whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm. [GOC:dph, ISBN:0124020607, ISBN:0198542771]
Catalysis of the reaction: ATP + H2O = ADP + phosphate, which promotes unfolding of protein substrates, and channel opening of the core proteasome. [GOC:rb, PMID:11430818]
Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs). [GOC:jl, GOC:txnOH, http://www.mblab.gla.ac.uk/, PMID:16858867]
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]
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 protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25. [GOC:bhm, GOC:pr, PMID:10872468, PMID:19450911]
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 joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi. [GOC:jid]
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]
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]
Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion. [GOC:mah, PMID:14570579]
Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein. [PMID:12642621]
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 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 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 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]
Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial electron transport, NADH to ubiquinone. [GO_REF:0000058, GOC:dph, GOC:TermGenie, PMID:23530063]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly. [GOC:mah]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. [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 deprivation of nourishment. [GOC:jl]
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 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]
Any process that stops, prevents or reduces the frequency, rate or extent of voltage-gated calcium channel activity. [GOC:BHF, GOC:TermGenie]
The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG). [GOC:dph, GOC:signaling, GOC:tb, PMID:12675914]
Any process that stops, prevents, or reduces 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 decreases the concentration of calcium ions in the cytosol. [GOC:ai]
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]
Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus. [GOC:jid]
Any process that results in a change in the behavior of an organism as a result of a cocaine stimulus. [GOC:jid]
Any process that modulates 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 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]
Any process that modulates the frequency, rate or extent of the regulated release of dopamine. [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 a toxic stimulus. [GOC:lr]
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/]
The series of molecular signals generated as a consequence of a dopamine 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]
Any process that stops, prevents, or reduces the frequency, rate or extent of adenylate cyclase activity. [GOC:go_curators]
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 process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. [GOC:dph]
Interacting selectively and non-covalently with dopamine, a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase from 3,4-dihydroxy-L-phenylalanine. [ISBN:0198506732]
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]
Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gi/Go to initiate a change in cell activity. [GOC:mah, ISBN:0953351033, IUPHAR_RECEPTOR:2254, IUPHAR_RECEPTOR:2256, IUPHAR_RECEPTOR:2258]
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 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 behavior in which an organism produces sounds by a mechanism involving its respiratory system. [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 stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the origin and formation of neurons. [GOC:ai]
Any process that stops, prevents or reduces 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 rate or extent of progression through the cell cycle. [GOC:dph, GOC:go_curators, GOC:tb]
Any process that activates or increases the frequency, rate or extent of neuron differentiation. [GOC:go_curators]
Female behaviors associated with the care and rearing of offspring. [GOC:curators]
The specific behavior of an organism in response to a novel environment or stimulus. [GOC:BHF, GOC:pr, PMID:11682103, PMID:9767169]
Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior]
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). [GOC:mah, GOC:mtg_apoptosis, PMID:25236395]
The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation. [http://hebb.mit.edu/courses/9.03/lecture4.html, ISBN:0582227089]
An acute behavioral change resulting from a perceived external threat. [GOC:dph, PMID:9920659]
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 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 cholesterol homeostasis. [GOC:BHF]
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]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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 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 axon part that is located adjacent to the nodes of Ranvier and surrounded by lateral loop portions of myelin sheath. [GOC:mah, GOC:mh, NIF_Subcellular:sao936144858]
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]
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 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]
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 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 sodium channel in a cell membrane whose opening is governed by the membrane potential. [ISBN:0198506732]
The process in which 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]
Any process that modulates the potential difference across a post-synaptic membrane. [GOC:dph, GOC:ef]
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 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]
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 modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. [GOC:mah]
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]
An action potential that occurs in a neuron. [GOC:dph, GOC:isa_complete, GOC:tb]
A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to changes in intracellular ion homeostasis, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis, PMID:11454444, PMID:16483738]
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
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 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 sodium 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 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]
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]
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 covalent attachment of a mannose residue to a substrate molecule. [GOC:cjm]
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 mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid. [GOC:ai, GOC:cjm]
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]
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]
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. [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 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]
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]
Enables the directed movement of proteins into, out of or within a cell, or between cells. [ISBN:0198506732]
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]
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 vascular endothelial growth factor signaling pathway. [GOC:TermGenie]
The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium. [GOC:go_curators]
Any process that increases the extent to which blood vessels can be pervaded by fluid. [GOC:jl]
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]
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 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]
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 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]
Any process that activates or increases the frequency, rate or extent of signaling in response to detection of lipopolysaccharide. [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]
A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug. [http://www.graylab.ac.uk/omd/]
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 copper (Cu) ions. [GOC:ai]
The cytosolic iron-sulfur protein assembly (CIA) complex mediates the incorporation of iron-sulfur clusters into apoproteins involved in DNA metabolism and genomic integrity. [GOC:sp, PMID:22678362]
A homeostatic process involved in the maintenance of an internal steady state of oxygen within an organism or cell. [GOC:rph]
The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster. [GOC:jl, GOC:mah, GOC:pde, GOC:vw]
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 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]
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]
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 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]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, 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]
Formation of myofibrils, the repeating units of striated muscle. [GOC:mah]
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 telethonin, a protein found in the Z disc of striated muscle and which is a substrate of the titin kinase. [GOC:mah, PMID:10481174]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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]
Functions to control the survival, growth, differentiation and effector function of tissues and cells. [ISBN:0198599471]
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 the modulates the frequency, rate or extent of chromatin assembly. Chromatin assembly is the assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus. [GOC:dph, GOC:tb]
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 a histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity. [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 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 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 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: 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]
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 process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration. [GOC:BHF, GOC:dph, GOC:tb]
Interacting selectively and non-covalently with an identical protein or proteins. [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]
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 modulates the frequency, rate or extent of the directed movement of a MAP kinase from the nucleus to the cytoplasm. [GOC:dgf]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade. [GOC:go_curators]
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]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [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]
A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25. [GOC:bhm, GOC:pr, PMID:10872468, PMID:19450911]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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 joining of 2 or more lipid bilayer membranes that surround the endoplasmic reticulum. [GOC:elh, 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 endoplasmic reticulum. [GOC:dph, GOC:jl, GOC:mah]
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]
Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion. [GOC:mah, PMID:14570579]
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 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 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 directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages. [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]
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]
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]
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 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]
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 volume enclosed by the membranes of the endoplasmic reticulum. [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 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 process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane. [GOC:mah]
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]
The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release. [GOC:rb]
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]
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]
A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix. [ISBN:0198547684]
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 collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes. [ISBN:0721639976, PMID:19693541, PMID:21421911]
A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911]
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 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 whose specific outcome is the progression of the glomerular basement membrane over time, from its formation to the mature structure. The glomerular basement membrane is the basal laminal portion of the glomerulus which performs the actual filtration. [GOC:sr]
The action of a molecule that contributes to the structural integrity of the extracellular matrix. [GOC:mah]
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 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]
Any process that stops, prevents or reduces the frequency, rate or extent of voltage-gated calcium channel activity. [GOC:BHF, GOC:TermGenie]
The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG). [GOC:dph, GOC:signaling, GOC:tb, PMID:12675914]
Any process that stops, prevents, or reduces 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 decreases the concentration of calcium ions in the cytosol. [GOC:ai]
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]
Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus. [GOC:jid]
Any process that results in a change in the behavior of an organism as a result of a cocaine stimulus. [GOC:jid]
Any process that modulates 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 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]
Any process that modulates the frequency, rate or extent of the regulated release of dopamine. [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 a toxic stimulus. [GOC:lr]
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/]
The series of molecular signals generated as a consequence of a dopamine 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]
Any process that stops, prevents, or reduces the frequency, rate or extent of adenylate cyclase activity. [GOC:go_curators]
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 process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. [GOC:dph]
Interacting selectively and non-covalently with dopamine, a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase from 3,4-dihydroxy-L-phenylalanine. [ISBN:0198506732]
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]
Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gi/Go to initiate a change in cell activity. [GOC:mah, ISBN:0953351033, IUPHAR_RECEPTOR:2254, IUPHAR_RECEPTOR:2256, IUPHAR_RECEPTOR:2258]
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 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 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]
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 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]
Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation. [GOC:mah]
The process in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically mediate repression of translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs [PMID:14744438, PMID:15196554]
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]
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 complex containing both protein and micro-RNA (miRNA) molecules. miRNAs are approximately 22 nucleotide noncoding RNAs derived from endogenous genes; they are processed from the stem of a longer hairpin like structure termed a pre-miRNA. [GOC:bf, PMID:14559182]
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 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]
Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA. [PMID:14744438, PMID:15066275, PMID:15066283, PMID:23209154]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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 sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. [http://www.graylab.ac.uk/omd/, 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 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]
Any process that stops, prevents or reduces the frequency, rate or extent of cAMP-dependent protein kinase activity. [GOC:obol]
The acquisition and processing of information and/or the storage and retrieval of this information over time. [GOC:jid, PMID:8938125]
Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A. [GOC:mah]
Modulation of the activity of the enzyme cAMP-dependent protein kinase. [GOC:ai]
Stops, prevents or reduces the activity of a cAMP-dependent protein kinase. [GOC:mah]
An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer. [EC:2.7.11.11, ISBN:0198506732]
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 cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate). [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]
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]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation 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:mah, ISBN:0198506732]
The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. [ISBN:0198547684]
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 chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring. [GOC:ai]
Catalysis of the reaction: prostaglandin H(2) = prostaglandin E(2). [EC:5.3.99.3, RHEA:12896]
Interacting selectively and non-covalently with glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine. [GOC:bf, ISBN:0198506732]
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. [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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A series of molecular signals initiated by the binding of the peptide hormone prolactin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:nhn, GOC:signaling, PMID:21664429]
Any process that initiates the activity of the inactive transmembrane receptor protein tyrosine kinase activity. [GOC:dph, GOC:tb]
Interacting selectively and non-covalently with any peptide with hormonal activity in animals. [GOC:jl, ISBN:0198506732]
Combining with prolactin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:mah, GOC:signaling]
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]
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]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
A protein complex that contains the BRCA1-BARD1 heterodimer, RAP80/UIMC1, BRCC3/BRCC36, BRE/BRCC45, FAM175A/CCDC98/Abraxas and MERIT40/NBA1, and specifically recognizes and binds K63-linked polyubiquitin chains present on histone H2A and H2AX at DNA damage sites. [GOC:mah, PMID:19261749]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
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 deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a lysine residue in histone H2A or the variant H2AX. [GOC:mah, PMID:19202061, PMID:19214193]
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 DNA repair. [GOC:go_curators]
A cell cycle checkpoint that detects and negatively regulates progression from G2 to M phase in 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 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 repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix. [GOC:elh]
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 a histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity. [GOC:jl]
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 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 the basement membrane. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation. [GOC:go_curators]
The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells. [GOC:mah, ISBN:0815316194]
Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix. [GOC:mah, ISBN:0815316194]
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 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 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]
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]
A conserved protein complex that plays an important role in coupling deadenylation and decapping in the 5'-to-3' mRNA decay pathway. An example is found in S. cerevisiae. [GOC:jd, PMID:24139796]
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]
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 spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation. [GOC:ab, GOC:krc, GOC:mah, PMID:17332742, PMID:19239890]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
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]
A ribonucleoprotein complex that contains small nuclear RNA U6. [GOC:krc, GOC:mah]
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]
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]
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 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 process that is carried out at the cellular level which results in the separation of a single continuous mitochondrial membrane into two membranes and contributes to mitochondrial fission. [GOC:ascb_2009, GOC:dph, 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]
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]
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 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]
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]
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 modulates the frequency, rate or extent of the passage or uptake of molecules by the mitochondrial membrane. [GOC:bf]
The directed movement of ATP, adenosine triphosphate, 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 ADP, adenosine diphosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The morphological and physiological alterations undergone by mitochondria during apoptosis. [GOC:mah, GOC:mtg_apoptosis]
Catalysis of the reaction: ATP(out) + ADP(in) = ATP(in) + ADP(out). [TC:2.A.29.1.1]
The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. [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: UDP-glucose + (1,4)-alpha-D-glucosyl(n) = UDP + (1,4)-alpha-D-glucosyl(n+1). [EC:2.4.1.11]
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]
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 process of introducing a phosphate group on to a protein. [GOC:hb]
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]
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 activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
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 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]
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]
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 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]
The lipid bilayer surrounding any membrane-bounded vesicle in the cell. [GOC:mah, GOC:vesicle]
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]
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 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 process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers. [GOC:dph, GOC:jid, GOC:tb, http://www.mercksource.com, PMID:11891290]
The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium. [GOC:go_curators]
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 stops, prevents, or reduces 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]
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 activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity. [GOC:go_curators]
The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system. [GOC:ef]
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 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 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 any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments. [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
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 monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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 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 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 nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. [GOC:dph, GOC:tb]
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]
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 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 deoxyribonucleic acid. [GOC:mah, ISBN:0198547684]
Catalysis of the endonucleolytic cleavage of DNA to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end products. [EC:3.1.21.1]
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]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
Mitochondrial inner membrane complex involved in maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. In Saccharomyces cerevisiae the complex has six subunits: MIC10, MIC12, MIC19, MIC26, MIC27, and MIC60. [GOC:dph, PMID:21944719, PMID:21987634, PMID:22009199, PMID:24687277]
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 synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell. [GOC:dph, GOC:ef]
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]
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 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]
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]
The lipid bilayer surrounding a synaptic vesicle. [GOC:mah]
The component of the synaptic vesicle 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 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 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]
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]
Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished. [GOC:jid, GOC:lmg, GOC:mah, PMID:20448150]
A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity. [GOC:jid, http://www.mercksource.com, PMID:11891290]
A process that modulates long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers. [GOC:jid, http://www.mercksource.com, PMID:11891290]
A process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers. [GOC:jid, http://www.mercksource.com, PMID:11891290]
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 an identical protein or proteins. [GOC:jl]
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 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]
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 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 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 any of the compartments of the Golgi apparatus. [GOC:mah]
A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins. [GOC:curators, GOC:pr]
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 a galactosyl group to an acceptor molecule, typically another carbohydrate or a lipid. [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]
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]
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]
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]
The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping. [GOC:dos, 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]
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 part of a synapse that is part of the post-synaptic cell. [GOC:dos]
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]
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 chloride across a membrane. [GOC:TermGenie, 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]
The process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. [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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. [CHEBI:33709, GOC:ef, GOC:mlg]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
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 transmembrane transfer of an ion by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Enables the transmembrane transfer of a chloride ion by a channel that opens when extracellular glycine has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Interacting selectively and non-covalently with glycine, aminoethanoic acid. [GOC:ai]
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]
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 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]
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/]
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 lamellipodium morphogenesis. [GOC:BHF, GOC:mah]
Any process that activates or increases the frequency, rate or extent of wound healing, spreading of epidermal cells. [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:18394891]
Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading. [GOC:TermGenie, GOC:yaf]
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 cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the rate or extent of mammary gland epithelial cell proliferation. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of epithelial cell migration. [GOC:BHF, GOC:dph, GOC:tb]
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 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 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 any metal ion. [GOC:ai]
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 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]
Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory 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:krc]
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 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]
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]
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 methyl group is covalently attached to a molecule. [GOC:mah]
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]
The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. [GOC:hjd]
The process that results in the modification of the sugar of a nucleoside in tRNA at the 2'O position. [GOC:hjd, ISBN:155581073X]
Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor. [GOC:hjd]
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 methyl group from a donor to a nucleoside residue in a tRNA molecule. [GOC:mah]
Catalysis of the transfer of a methyl group to an acceptor molecule. [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 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 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 removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine. [GOC:bf]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
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]
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
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]
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 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 chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid. [GOC:go_curators]
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 any metal ion. [GOC:ai]
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]
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]
Catalysis of the reaction: H(2)O + leukotriene A(4) = leukotriene B(4). [EC:3.3.2.6, RHEA:22327]
Catalysis of the reaction: an epoxide + H2O = a glycol. [EC:3.3.2.10]
Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain. [GOC:jl, 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]
Any process that modulates the frequency, rate or extent of voltage-gated sodium channel activity. [GO_REF:0000059, GOC:TermGenie, PMID:24198377]
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. [GOC:dph, GOC:isa_complete, GOC:tb]
Any process pertaining to the functions of the nervous and muscular systems of an organism. [GOC:ai]
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 series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands. [GOC:ceb]
Locomotory behavior in a fully developed and mature organism. [GOC:ai]
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 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]
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 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]
Any process that modulates the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is 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. [GOC:tb]
The removal of a methyl group from one or more nucleotides within an DNA molecule. [PMID:17208187]
The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate. [GOC:BHF, GOC:mah, GOC:rl]
Any process that modulates the frequency, rate or extent of white fat cell proliferation. [GOC:mah, GOC:sl]
The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat. [GOC:dph]
Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system. [GOC:jl]
Any process that results in the repair of damaged RNA. [PMID:11000254, PMID:11070075, UniProtKB-KW:KW-0692]
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]
Removal of the methyl group from one or more nucleotides within a single-stranded RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms. [GOC:BHF, GOC:rl, PMID:18775698]
Removal of the methyl group from one or more nucleotides within a single-stranded DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms. [GOC:BHF, GOC:rl, PMID:18775698]
Any process that modulates 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]
The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT). [PMID:10946226]
A homeostatic process in which an organism modulates its internal body temperature. [GOC:jl]
Catalysis of the oxidative demethylation of N6-methyladenosine RNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N6-methyladenosine as formaldehyde. [PMID:22002720, PMID:26458103]
Catalysis of the oxidative demethylation of N1-methyladenine and N3-methylcytosine in DNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenine and N3-methylcytosine as formaldehyde. [IMG:00579, PMID:19786499]
Catalysis of the removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms. [PMID:12594517, PMID:16482161, PMID:18775698]
Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms. [PMID:12594517, PMID:16482161, PMID:18775698]
Interacting selectively and non-covalently with ferrous iron, Fe(II). [GOC:ai]
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 cations, charged atoms or groups of atoms with a net positive charge. [GOC:jl]
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]
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]
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]
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 biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [GOC:isa_complete]
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 an intronic sequence of a pre-messenger RNA (pre-mRNA). [GOC:ans, PMID:16260624]
Interacting selectively and non-covalently with the U12 small nuclear RNA (U12 snRNA). [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]
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 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]
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, 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 involving UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate. [GOC:ai]
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]
Catalysis of the transfer of an uridylyl group to an acceptor. [GOC:mah]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Catalysis of the reaction: alpha-D-glucose 1-phosphate + UTP = diphosphate + UDP-D-glucose. [EC:2.7.7.9, RHEA:19892]
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 leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
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 removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of cell migration. [GOC:go_curators]
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]
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 modulates the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity. [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]
Any cell cycle regulatory process that promotes the commitment of a cell from G1 to S phase of the mitotic cell cycle. [GOC:mtg_cell_cycle]
The covalent alteration of one or more nucleotides within snRNA, resulting in a change in the properties of the snRNA. [GOC:jl]
Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:bf, PMID:20404130]
The chemical reactions and pathways involving snRNA, small nuclear RNA, any of various low-molecular-mass RNA molecules found in the eukaryotic nucleus as components of the small nuclear ribonucleoprotein. [ISBN:0198506732]
Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor. [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]
Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate. [GOC:mah]
Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule. [GOC:mah]
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]
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 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 an anion 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]
The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage. [GOC:krc]
The directed movement of anions, atoms or small molecules with a net negative 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]
Enables the transfer of a negatively charged ion from one side of a membrane to the other. [GOC:dgf, 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: inorganic anion A(out) + inorganic anion B(in) = inorganic anion A(in) + inorganic anion B(out). [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]
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 process whose specific outcome is the progression of an auditory receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. [GOC:dph]
Any process that modulates the internal pH of a cell, measured by the concentration of the hydrogen ion. [GOC:ai, GOC:dph, GOC:tb]
The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:krc]
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]
Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. [GOC:txnOH]
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]
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]
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 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 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 the innate immune response, the organism's first line of defense against infection. [GOC:ebc]
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. [GOC:jl]
Any process that modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
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 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]
A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too. [GOC:bf, PMID:24587488]
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 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 cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives. [GOC:bf, GOC:ceb, ISBN:0198506732]
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 resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position. [CHEBI:26034, GOC:al, GOC:vw]
Any process that activates or increases the frequency, rate or extent of cell migration. [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 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]
Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+). [EC:2.7.1.153, RHEA:21295]
Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + 2 H(+). [EC:2.7.1.154, RHEA:18376]
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: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+). [EC:2.7.1.137, RHEA:12712]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II. [GOC:tb]
A protein complex that consists of only SMAD proteins; may be homomeric or heteromeric. [GOC:mah, PMID:9670020]
A transcriptionally active complex that binds to an activin response element (ARE) in the promoter of target genes, and is composed of two SMAD2 proteins, one SMAD4 protein and a Forkhead activin signal transducer (FAST) transcription factor. [PMID:12374795, PMID:9288972]
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]
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]
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 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 ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
Any process that activates or increases the frequency, rate or extent of histone H3-K9 acetylation. [GOC:BHF]
Any process that stops, prevents or reduces the frequency, rate or extent of cardiac myofibril assembly. [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:16151019]
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 process in which the anatomical structures of a nephrogenic mesenchymal tissue are generated and organized. Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron. [GOC:mtg_kidney_jan10]
The process in which the anatomical structures of a metanephric mesenchymal tissue are generated and organized. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros. [GOC:mtg_kidney_jan10]
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 transforming growth factor beta stimulus. [GOC:mah]
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]
A series of molecular signals initiated by the binding of interleukin-6 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:add, GOC:BHF, GOC:mah, GOC:signaling]
The process in which a female gonad is generated and organized. [GOC:BHF, GOC:dph]
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers. [GOC:mtg_heart]
Any process that decreases 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:BHF, GOC:dph, GOC:tb]
The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another. [GOC:dph]
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]
Any process that increases the rate, frequency or extent of SMAD protein import into the nucleus, i.e. the directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways. [GOC:BHF, GOC:dph, GOC:tb]
The reproductive developmental process whose specific outcome is the progression of the uterus over time, from its formation to the mature structure. [GOC:dph, GOC:ebc]
The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities. [GOC:dph, ISBN:0721662544]
Any process that modulates the frequency, rate or extent of hair follicle development. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. [GOC:mah]
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. [GOC:ai]
The process in which the limits of an anatomical structure are generated. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. [GO_REF:0000021, GOC:mtg_15jun06]
The process whose specific outcome is the progression of the sebaceous gland over time, from its formation to the mature structure. [GOC:jid]
The process in which the anatomical structures of a tissue are generated and organized. [GOC:dph, GOC:jid]
The process in which the developmental fate of a cell becomes restricted such that it will develop into a neuron. [GOC:dph]
The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the regulated release of follicle-stimulating hormone. [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 stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
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 frequency, rate or extent of cell proliferation. [GOC:jl]
The change in morphology and behavior of an endothelial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor. [GOC:mgi_curators, ISBN:0781735149, PMID:12851652, PMID:14581484]
The progression of the atrioventricular canal over time, from its formation to the mature structure. The atrioventricular canal is the part of the heart connecting the atrium to the cardiac ventricle. [GOC:BHF, GOC:gr, PMID:14701881, UBERON:0002087, ZFA:0001315]
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 the regulated release of luteinizing hormone. [GOC:mah]
Any process that modulates the frequency, rate, or extent of production of transforming growth factor-beta2. [GOC:mah]
The establishment, maintenance and elaboration of the rostro-caudal axis of a somite, prior to the morphological formation of a somite boundary. [GOC:bf, PMID:16326386, PMID:17360776]
Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity. [GOC:go_curators]
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 stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway. [GOC:mah]
The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell. [GOC:dh, GOC:ef]
Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways. [GOC:dph, GOC:tb]
Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is 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]
Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. [GOC:BHF, GOC:dph, GOC:tb]
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]
The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure. [GOC:dph, GOC:jid, 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]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. [GOC:dph, GOC:tb]
The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. [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]
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 union of male and female gametes to form a zygote. [GOC:ems, GOC:mtg_sensu]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
The aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins. [GOC:isa_complete]
A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:BHF, GOC:mah, GOC:signaling]
Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell. [GOC:ai, 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 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]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord. [GOC:dph]
The progression of a cardiac septum over time, from its initial formation to the mature structure. [GOC:mtg_heart]
Any process that increases the rate, frequency or extent of cell proliferation that contributes to the shaping of a heart valve. [GOC:mtg_heart]
The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized. [GOC:mtg_heart]
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 developmental process pertaining to the initial formation of the atrioventricular valve from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. [GOC:mtg_heart]
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 whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine. [GOC:dph, GOC:mtg_kidney_jan10, ISBN:0124020607, ISBN:0721662544]
A gastrulation process in which the initial invagination becomes the anus and the mouth forms second. [GOC:go_curators, GOC:mtg_sensu]
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]
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]
The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules. [GOC:dph, PMID:16916378]
The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure. [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 a receptor-regulated SMAD signaling protein. [GOC:BHF, GOC:vk, PMID:19114992]
Interacting selectively and non-covalently with an inhibitory SMAD signaling protein. [GOC:BHF, GOC:vk, PMID:19114992]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
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 an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
A TGF-beta cytoplasmic mediator that forms a complex with a phosphorylated pathway-specific mediator. The heterocomplex translocates to the nucleus to regulate transcription. [GOC:hjd]
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]
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 the transcription regulatory 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:krc]
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II. [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 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]
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 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 cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. [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]
A protein complex that associates with mRNP particles and RNA polymerase II and is proposed to integrate transcript elongation with the regulation of alternative splicing. In humans it is composed of the proteins KIAA1967/DBC1 and ZNF326/ZIRD. [GOC:sp, PMID:22446626]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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]
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 ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
Any process that activates or increases the frequency, rate or extent of a DNA damage checkpoint. [GOC:obol]
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 modulates the rate, frequency, or extent of protein deacetylation, the removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. [GOC:tb]
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 stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The change in the morphology of the mitochondria in an apoptotic cell from a highly branched network to a fragmented vesicular form. [GOC:mtg_apoptosis, GOC:rk, PMID:12867994]
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 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]
Any process that modulates 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 a DNA-dependent RNA polymerase. [GOC:mah, GOC:txnOH]
Any process that stops, prevents, or reduces 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]
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 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]
The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GOC:krc, GOC:mah]
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 enzyme. [GOC:jl]
Binds to and stops, prevents or reduces the activity of an enzyme. [GOC:ai, GOC:ebc]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits. [GOC:txnOH]
The component of the endoplasmic reticulum 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:curators, GOC:dos]
A vesicle with a coat formed of the COPI coat complex proteins. COPI-coated vesicles are found associated with Golgi membranes at steady state, are involved in Golgi to endoplasmic reticulum (retrograde) vesicle transport, and possibly also in intra-Golgi transport. [GOC:mah, PMID:11252894]
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]
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]
Interacting selectively and non-covalently with an unfolded protein. [GOC:ai]
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 telomere capping. [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:23959892]
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]
A series of molecular signals in which a stress-activated MAP kinase cascade relays one or more of the signals; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase. [GOC:ai, PMID:15936270]
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 tumor necrosis factor stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase. [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 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 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]
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 an increase or decrease in the concentration of solutes outside the organism or cell. [GOC:jl]
The process of introducing a phosphate group on to a protein. [GOC:hb]
The initiation of the activity of the inactive enzyme MAP kinase (MAPK). [PMID:9561267]
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 any enzyme. [GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the concomitant phosphorylation of threonine (T) and tyrosine (Y) residues in a Thr-Glu-Tyr (TEY) thiolester sequence in a MAP kinase (MAPK) substrate. [ISBN:0198547684]
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]
Interacting selectively and non-covalently with magnesium (Mg) 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]
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 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]
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 the provision of a combination of complex inanimate and social stimulations in the organism's housing environment. [GOC:sl, PMID:23644055, PMID:25934034]
Any process that modulates the frequency, rate or extent of a dopamine receptor signaling pathway activity. A dopamine receptor signaling pathway is the series of molecular signals generated as a consequence of a dopamine receptor binding to one of its physiological ligands. [GOC:dph]
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]
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 modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The response to external or internal stimuli that results in the locomotory process of swimming. Swimming is the self-propelled movement of an organism through the water. [GOC:cvs, PMID:16764679]
Behavior in a fully developed and mature organism. [GOC:mah, ISBN:0877797099]
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 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 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]
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 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 of introducing a phosphate group on to a protein. [GOC:hb]
The initiation of the activity of the inactive enzyme MAP kinase (MAPK). [PMID:9561267]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
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]
The process in which an adenosine in position 34 of a tRNA is post-transcriptionally converted to inosine. [GOC:hjd, ISBN:155581073X]
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 reaction: adenosine + H2O = inosine + NH3, in a tRNA molecule. [GOC:mah, IMG:00700]
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 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 ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins. [GOC:krc, GOC:vw, PMID:12068309, PMID:12957375, PMID:15120992, PMID:15590835]
A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs. [ISBN:0879695897, PMID:17284456]
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 class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA. [NIF_Subcellular:nlx_subcell_090901, PMID:10944589, PMID:11031238, PMID:7559785]
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 structure found in the nucleolus, which contains nearly completed preribosomal particles destined for the cytoplasm. [PMID:10754561]
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 modification of a histone by addition of a methyl group to an glutamine residue. [PMID:24352239]
Any process in which small nucleolar RNA is transported to, or maintained in, a specific location. [ISBN:0716731363]
The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule. [GOC:mah]
The chemical reactions and pathways involving snoRNA, small nucleolar RNA, any of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA. [GOC:krc]
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 involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. [GOC:curators]
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]
Any process involved in forming the mature 3' end of a box C/D snoRNA molecule. [GOC:krc]
Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine. [PMID:24352239]
Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP. [GOC:ai]
Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule. [GOC:mah]
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]
Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor. [GOC:krc, PMID:16858867]
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]
Interacting selectively and non-covalently with a G-protein coupled receptor. [GOC:ceb, 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]
Transient adhesive interactions between leukocytes and endothelial cells lining blood vessels. Carbohydrates on circulating leukocytes bind selectins on the vessel wall causing the leukocytes to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between selectins and their ligands. Typically the first step in cellular extravasation (the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection). [GOC:bf, ISBN:0781735149, PMID:14680625, PMID:14708592, PMID:7507411, PMID:8600538, Wikipedia:Leukocyte_extravasation]
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 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 network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum. [ISBN:0198506732, 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 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 membrane that surrounds the acrosomal lumen. The acrosome is a special type of lysosome 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. [GOC:dph]
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. [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 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 the Golgi apparatus. [GOC:dph, GOC:jl, GOC:mah]
A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins. [GOC:curators, GOC:pr]
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage. [GOC:ascb_2009, GOC:dph, GOC:tb]
The progression of the ventricular septum over time from its formation to the mature structure. [GOC:mtg_heart]
The process of directing proteins towards the Golgi; usually uses signals contained within the protein. [GOC:ai, GOC:mah]
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 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]
Any process that stops, prevents or reduces the frequency, rate or extent of voltage-gated calcium channel activity. [GOC:BHF, GOC:TermGenie]
The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG). [GOC:dph, GOC:signaling, GOC:tb, PMID:12675914]
Any process that stops, prevents, or reduces 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 decreases the concentration of calcium ions in the cytosol. [GOC:ai]
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]
Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus. [GOC:jid]
Any process that results in a change in the behavior of an organism as a result of a cocaine stimulus. [GOC:jid]
Any process that modulates 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 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]
Any process that modulates the frequency, rate or extent of the regulated release of dopamine. [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 a toxic stimulus. [GOC:lr]
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/]
The series of molecular signals generated as a consequence of a dopamine 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]
Any process that stops, prevents, or reduces the frequency, rate or extent of adenylate cyclase activity. [GOC:go_curators]
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 process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. [GOC:dph]
Interacting selectively and non-covalently with dopamine, a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase from 3,4-dihydroxy-L-phenylalanine. [ISBN:0198506732]
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]
Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gi/Go to initiate a change in cell activity. [GOC:mah, ISBN:0953351033, IUPHAR_RECEPTOR:2254, IUPHAR_RECEPTOR:2256, IUPHAR_RECEPTOR:2258]
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]
An adherens junction which connects a cell to another cell. [GOC:hb]
The orderly movement of an epithelial cell from one site to another, often during the development of a multicellular organism. [GOC:ascb_2009, GOC:BHF, GOC:dph, GOC:tb]
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 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]
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 cardioblast proliferation in the second heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. The secondary heart field is the region of the heart that will form the majority of the mesodermal component of the right ventricle, the arterial pole (outflow tract) and the venous pole (inflow tract). [GOC:BHF, GOC:mah, GOC:rl]
The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another. [GOC:dph, GOC:mtg_heart]
Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation. [GOC:dph, GOC:rph]
Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation. [GOC:dph, GOC:rph]
The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery. [GOC:dph, GOC:rph, PMID:15138308, PMID:16376438]
The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. [GOC:devbiol, GOC:mtg_heart]
Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. [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]
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]
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]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. [GOC:go_curators]
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]
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 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 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]
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 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]
The progression of the atrial septum over time, from its initial formation to the mature structure. [GOC:mtg_heart]
The progression of the ventricular septum over time from its formation to the mature structure. [GOC:mtg_heart]
The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure. [GOC:mtg_heart]
The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts. [GOC:mtg_heart]
The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. [GOC:mtg_heart]
The process in which the structure of the atrioventricular valve is generated and organized. [GOC:mtg_heart]
The process whose specific outcome is the progression of the bundle of His over time, from its formation to the mature structure. The bundle of His is part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers. [GOC:mtg_heart]
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]
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 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 the transcription regulatory 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:krc]
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]
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]
Any process that modulates the frequency, rate or extent of T cell activation. [GOC:ai]
The process of regulating the proliferation and elimination of T cells such that the total number of T cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. [GOC:mgi_curators, ISBN:0781735149]
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 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 a kinase, any enzyme that catalyzes the transfer of a phosphate group. [GOC:jl]
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]
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 protein targeting to mitochondrion. [GO_REF:0000058, GOC:pad, GOC:PARL, GOC:TermGenie, PMID:24270810]
Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy). [GO_REF:0000058, GOC:autophagy, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24600391]
A mitotic cell cycle checkpoint that originates from the spindle and delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and oriented, the completion of anaphase until chromosomes are attached to the spindle, or mitotic exit and cytokinesis when the spindle does not form. [GOC:mtg_cell_cycle]
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 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]
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]
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 protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. [GOC:jl]
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 modulates the frequency, rate or extent of cardiac cell fate specification. [GOC:BHF]
Any process that modulates the frequency, rate or extent of stem cell division. [GOC:obol]
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]
Any process that modulates the frequency, rate or extent of stem cell proliferation. 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. [GOC:mtg_kidney_jan10]
The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels. [GOC:mtg_kidney_jan10, GOC:yaf, http://en.wikibooks.org/wiki/Human_Physiology/The_Urinary_System]
The process in which the anatomical structures of the endodermal digestive tract are generated and organized. The endodermal digestive tract includes those portions of the digestive tract that are derived from endoderm. [GOC:dph, GOC:yaf]
The progression of the gall bladder over time, from its initial formation to the mature structure. The gall bladder is a cavitated organ that stores bile. [GOC:dph]
The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gall bladder. The common bile duct transports bile from the liver and gall bladder to the intestine. [PMID:20614624]
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers. [GOC:mtg_heart]
The process involved in cardiac cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment. [GOC:mtg_heart]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that ultimately results in a cell being specified to adopt a definitive endodermal cell fate. [GOC:dph, GOC:sdb_2009, GOC:tb]
Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. [GOC:bf, GOC:dph, PMID:17722983]
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. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes. [GOC:bf, GOC:dph, PMID:11532397, PMID:19619488]
Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation. [GOC:ai]
The process in which a cell becomes capable of differentiating autonomously into a stem cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed. [CL:0000034, GOC:isa_complete]
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 activates, maintains or increases the rate of skeletal muscle tissue development. [GOC:go_curators]
The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase. [GOC:jid, GOC:rc]
Development, taking place during the embryonic phase, 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:jid]
Any process that modulates the frequency, rate or extent of embryonic development. [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 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]
Any process that activates or increases the frequency, rate or extent of cell differentiation. [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]
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]
Any process that stops, prevents, or reduces the frequency, rate or extent of mesoderm cell fate specification. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of mesoderm cell fate specification. [GOC:go_curators]
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]
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 decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway. [GOC:dph, GOC:go_curators, 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 in which the neural tube is divided into specific regions along the rostrocaudal axis. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869]
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 cell fate determination process in which a cell becomes capable of differentiating autonomously into an endoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed. [GOC:go_curators, ISBN:0878932437]
The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. [GOC:dph, GOC:tb]
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 process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that decreases the rate, frequency, or extent of the series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time. [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]
The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart. [GOC:mtg_heart]
The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field. [GOC:mtg_heart]
The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation. [GOC:dph, PMID:12094232]
The morphogenesis of cells in the inner cell mass. [GOC:dph, ISBN:0124020607, ISBN:0198542771]
The formation of the endoderm during gastrulation. [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]
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]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
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 a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with the beta subunit of the catenin complex. [GOC:bf]
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 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 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 the transcription regulatory 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:krc]
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]
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, 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 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]
Catalysis of the hydrolysis of any glycosyl bond. [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 random hydrolysis of (1->4) linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate. [EC:3.2.1.35]
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 frequency, rate or extent of intrinsic apoptotic signaling pathway. [GOC:mtg_apoptosis]
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]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [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]
Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation. [GOC:dph]
Any process that stops, prevents or reduces the frequency, rate or extent of meiotic cell cycle phase transition. [GOC:mtg_cell_cycle, GOC:TermGenie, PMID:22841721]
The process in which a germline cell switches cell cycle mode from mitotic to meiotic division. [GOC:ai]
The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue. [GOC:jl, UBERON:0002097]
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]
The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. [GOC:dph, GOC:tb]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine. [GOC:dph, GOC:mtg_kidney_jan10, ISBN:0124020607, ISBN:0721662544]
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 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]
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]
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 spliceosomal complex that contains the U2, U5 and U6 snRNPs 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 U2, U5 and U6 snRNPs. [GOC:ab, GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393, PMID:18322460, PMID:19239890]
A spliceosomal complex that is formed by the displacement of the U1 and U4 snRNPs from the precatalytic spliceosome; the U2, U5 and U6 snRNPs remain associated with the mRNA. This complex, sometimes called the activated spliceosome, is the catalytically active form of the spliceosome, and includes many proteins in addition to those found in the U2, and U5 and U6 snRNPs. [GOC:ab, GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393, PMID:18322460, PMID:19239890]
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 protein complex consisting of Prp19 and associated proteins that is involved in the transition from the precatalytic spliceosome to the activated form that catalyzes step 1 of splicing, and which remains associated with the spliceosome through the second catalytic step. It is widely conserved, found in both yeast and mammals, though the exact composition varies. In S. cerevisiae, it contains Prp19p, Ntc20p, Snt309p, Isy1p, Syf2p, Cwc2p, Prp46p, Clf1p, Cef1p, and Syf1p. [GOC:krc, PMID:16540691, PMID:19239890]
Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. [GOC:tb]
The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript. [GOC:krc, http://calspace.ucsd.edu/origins/Glossary/C.htm, ISBN:0879695897]
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 activates or increases the frequency, rate or extent of RNA splicing. [GOC:mah]
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]
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 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 any metal ion. [GOC:ai]
Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA molecule. [GOC:bf, GOC:kmv, PMID:21901112, SO:0000120]
Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 snRNA). [GOC:mah]
Enables the directed movement of substances between the nucleus and the cytoplasm of a cell. [GOC:ai]
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]
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]
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 directed movement of mRNA, messenger ribonucleic acid, 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]
The directed movement of mRNA from the nucleus to the cytoplasm. [GOC:ma]
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]
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 protein complex that contains two proteins (know in several organisms, including Drosophila, as NXF1 and NXF2) and is required for the export of the majority of mRNAs from the nucleus to the cytoplasm; localized in the nucleoplasm and at both the nucleoplasmic and cytoplasmic faces of the nuclear pore complex; shuttles between the nucleus and the cytoplasm. [PMID:11780633]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm. [GOC:ai]
An ion channel complex through which calcium ions pass. [GOC:mah]
Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions. [GOC:bf, PMID:18397324]
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-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions. [GOC:bf, GOC:go_curators]
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-5-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 5' position. [GOC:bf, GOC:tair_curators]
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 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]
A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins. [GOC:krc, GOC:vw, PMID:12068309, PMID:12957375, PMID:15120992, PMID:15590835]
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 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]
Interacting selectively and non-covalently with U3 small nucleolar RNA. [GOC:mah]
Interacting selectively and non-covalently with ribosomal RNA. [GOC:jl]
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]
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 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]
The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. [ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid. [CHEBI:17115, GOC:ai, GOC:jsg]
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 amino group to an acceptor, usually a 2-oxo acid. [ISBN:0198506732]
Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate. [EC:2.6.1.52]
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]
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]
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 any membrane-bounded vesicle in the cell. [GOC:mah, GOC:vesicle]
The lipid bilayer surrounding an endosome. [GOC:mah]
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 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 modulates the frequency, rate or extent of autophagosome assembly. [GOC:autophagy, GOC:BHF]
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]
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 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]
A process in which a protein is transported to, or maintained in, a location within the nucleus. [GOC:ecd]
The process in which the wraps of cell membrane that constitute myelin are laid down around an axon in the central or peripheral nervous system. [GOC:dgh, GOC:dph, GOC:tb]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ADP + 2 H(+). [EC:2.7.1.68, RHEA:14428]
Catalysis of the reaction: ATP + a phosphatidylinositol phosphate = ADP + a phosphatidylinositol bisphosphate. [EC:2.7.1.-, PMID:9759495]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + 2 H(+). [EC:2.7.1.150, RHEA:13612]
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]
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]
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 synaptic vesicle clustering. [PMID:21513708]
The receptor clustering process involved in assembly of the postsynaptic membrane in which neuroligins are localized to distinct domains in the cell membrane. Neuroligins are neuronal cell surface proteins on the postsynaptic membrane that mediate synapse formation between neurons. [GOC:BHF, GOC:sjp, PMID:12796785]
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]
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]
Any process that stops, prevents, or reduces 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 activity of a phosphoprotein phosphatase. [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 process that activates or increases the frequency, rate or extent of receptor internalization. [GOC:hjd]
Interacting selectively and non-covalently with a type II activin receptor. [GOC:BHF, GOC:vk]
Interacting selectively and non-covalently with a SMAD signaling protein. [GOC:ai]
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 a beta-1 adrenergic receptor. [GOC:mah, GOC:nln]
Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex. [GOC:mah]
Interacting selectively and non-covalently with any phosphatase. [GOC:jl]
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 part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
Reactions triggered in response to the presence of a virus that act to protect the cell or organism. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication. [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 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 from a virus. [GOC:hb]
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 chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. [ISBN:0198506732]
Catalysis of the transfer of a nucleotidyl group to a reactant. [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]
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 double-stranded RNA. [GOC:jl]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Catalysis of the reaction: ATP = pppA(2'p5'A)n oligomers. This reaction requires the binding of double-stranded RNA. [ISBN:0198506732]
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]
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]
Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion. [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 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 interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far. [GOC:mah, PR:000000017]
The attachment of a cell to a cell of a different type via adhesion molecules. [GOC:add]
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 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]
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]
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]
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]
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 outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope. [GOC:ai]
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 (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound 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 exogenous double-stranded RNA 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 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 activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. [GOC:jl]
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-beta stimulus. Interferon-beta is a type I interferon. [GOC:sl, PR:000024939]
Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:mah]
The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. [GOC:add, GOC:mah]
Any process that activates or increases the frequency, rate or extent of protein binding. [GOC:mah]
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 process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, GOC:mtg_sensu, ISBN:0781735149, PMID:15199967, PMID:16177805]
Interacting selectively and non-covalently with cyclic-GMP-AMP (cGAMP) cyclic nucleotide. [GOC:dph, PMID:23258412]
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 cyclic-di-GMP, cyclic dimeric guanosine monophosphate. [CHEBI:49537, GOC:bf]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
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 transcription factor, any protein required to initiate or regulate transcription. [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]
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 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 modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
The discharge, by sperm, of a single, anterior secretory granule following the sperm's attachment to the zona pellucida surrounding the oocyte. The process begins with the fusion of the outer acrosomal membrane with the sperm plasma membrane and ends with the exocytosis of the acrosomal contents into the egg. [GOC:dph, PMID:3886029]
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 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 filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. [GOC:mah, ISBN:0198506732, PMID:10666339]
A form of the tropomyosin dimer found associated with actin and the troponin complex in muscle thin filaments. [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 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 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 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]
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 frequency, rate or extent of epidermal growth factor receptor signaling pathway activity. [GOC:go_curators]
A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins. [GOC:ecd, GOC:mah]
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 multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
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]
Interacting selectively and non-covalently with the epidermal growth factor receptor. [GOC:ai]
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]
A protein complex that possesses activity that prevents or downregulates transcription. [GOC:mah]
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]
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]
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 a histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity. [GOC:jl]
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 zinc (Zn) ions. [GOC:ai]
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]
Interacting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery. [GOC:krc]
Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
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 chemical reactions and pathways involving the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands. [ISSN:09498257]
The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands. [http://www.sunysb.edu/biochem/BIOCHEM/facultypages/schindelin/, ISSN:09498257, PMID:22370186, PMID:23201473]
Catalysis of the reaction: 2 H+ + MoO2-molybdopterin cofactor(2-) + L-cysteine  <=> thio-molybdenum cofactor + L-alanine  + H2O [EC:2.8.1.9]
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]
Interacting selectively and non-covalently with molybdenum (Mo) ions. [GOC:ai]
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 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 sulfurylation of the desulfo form of molybdenum cofactor (MoCo), a cofactor required for the activity of some enzymes, such as aldehyde oxidase. [GOC:mah, PMID:11549764]
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 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]
The portion of the plasma membrane surrounding a ruffle. [GOC:mah]
A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. [GOC:mtg_apoptosis, http://en.wikipedia.org/wiki/Bleb_(cell_biology), PMID:12083798, PMID:16624291]
A two-stranded helical polymer of the protein actin. [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]
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]
A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. [GOC:mah, ISBN:0198506732, PMID:10666339]
A form of the tropomyosin dimer found associated with actin and the troponin complex in muscle thin filaments. [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]
A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber. [PMID:16651381]
Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell migration. [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:20693317]
Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell proliferation. [GO_REF:0000058, GOC:TermGenie, PMID:23246467]
Muscle contraction of cardiac muscle tissue. [GOC:dph]
The process in which the anatomical structures of cardiac ventricle muscle is generated and organized. [GOC:devbiol]
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 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 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 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 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 process in which the secretion of epinephrine into the bloodstream or released from nerve endings increases the rate of heart muscle contraction. [GOC:mtg_cardio, GOC:rl]
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 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]
Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton). [GOC:mah]
The highly organized segment of the sperm flagellum which begins at the connecting piece and is characterized by the presence of 9 outer dense fibers (ODFs) that lie outside each of the 9 outer axonemal microtubule doublets and by a sheath of mitochondria that encloses the ODFs and the axoneme; the midpiece terminates about one-fourth of the way down the sperm flagellum at the annulus, which marks the beginning of the principal piece. [GOC:cjm, MP:0009831]
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 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]
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 multimeric complex connected to a microtubule. [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 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 double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy. [GOC:autophagy, ISBN:0198547684, PMID:11099404]
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]
The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered. [GOC:autophagy, GOC:isa_complete]
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 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 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 the gamma-aminobutyric acid (GABA, 4-aminobutyrate) receptor. [GOC:ai]
Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin. [GOC:krc]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
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]
Catalysis of the hydrolysis of any acid anhydride. [GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5. [GOC:sp, PMID:15960975]
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/]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process. [GOC:mtg_apoptosis, GOC:obol, GOC:yaf]
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 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. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes. [GOC:bf, GOC:dph, PMID:11532397, PMID:19619488]
The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III promoter. [GOC:go_curators, GOC:txnOH]
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 cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors. [GOC:jl, PMID:12042764]
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 stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway. [GOC:dph, GOC:go_curators, GOC:tb]
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 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]
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 histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity. [GOC:jl]
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]
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 the beta subunit of the catenin complex. [GOC:bf]
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]
Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix. [GOC:jl, 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 one of the p53 family of proteins. [GOC:hjd]
A dendrite that emerges near the apical pole of a neuron. In bipolar neurons, apical dendrites are located on the opposite side of the soma from the axon. [NIF_Subcellular:sao273773228]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
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]
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. [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 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 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 dendrite development. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of dendrite development. [GOC:TermGenie]
Any process that modulates the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound. [GOC:dph, GOC:tb]
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]
The process that organizes a synapse so that it attains its fully functional state. Synaptic maturation plays a critical role in the establishment of effective synaptic connections in early development. [GOC:dph, GOC:ef]
Any process that modulates the frequency, rate or extent of dendrite development. [GOC:ai]
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]
Locomotory behavior in a fully developed and mature organism. [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 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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits. [GOC:ecd]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cell envelope, everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present. [GOC:jl]
The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte. [GOC:dph, GOC:mah, GOC:sdb_2009, GOC:tb]
The formation of a covalent cross-link between or within protein chains. [GOC:jsg]
Interacting selectively and non-covalently with calcium ions (Ca2+). [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]
Catalysis of the reaction: protein glutamine + alkylamine = protein N5-alkylglutamine + NH3. This reaction is the formation of the N6-(L-isoglutamyl)-L-lysine isopeptide, resulting in cross-linking polypeptide chains; the gamma-carboxamide groups of peptidyl-glutamine residues act as acyl donors, and the 6-amino-groups of peptidyl-lysine residues act as acceptors, to give intra- and intermolecular N6-(5-glutamyl)lysine cross-links. [EC:2.3.2.13, RESID:AA0124]
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]
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]
A multisubunit chaperone that is capable of delivering unfolded proteins to cytosolic chaperonin, which it acts as a cofactor for. In humans, the complex is a heterohexamer of two PFD-alpha and four PFD-beta type subunits. In Saccharomyces cerevisiae, it also acts in the nucleus to regulate the rate of elongation by RNA polymerase II via a direct effect on histone dynamics. [GOC:jl, PMID:17384227, PMID:24068951, PMID:9630229]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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]
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 unfolded protein. [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]
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 process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
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]
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]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:mah]
The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland. [GOC:dph]
The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a thyroid-stimulating hormone-secreting cell. A thyroid-stimulating hormone-secreting cell is a basophil cell of the anterior pituitary that produces thyroid-stimulating hormone, thyrotrophin. [GOC:dph]
The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a corticotropic hormone secreting cell. An corticotropic hormone secreting cell is a basophil cell of the anterior pituitary that produces corticotropin. [GOC:dph]
Any process that activates or increases 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]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
Any process that activates or increases the rate or extent of epithelial cell proliferation. [GOC:ai]
The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate. [CL:0000034, GOC:isa_complete]
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 axon injury stimulus. [GOC:dgh, GOC:dph, GOC:jid, GOC:lm]
Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina. [GOC:ai, GOC:tb]
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 activates or increases the frequency, rate or extent of osteoblast differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of cell differentiation. [GOC:go_curators]
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 that activates or increases the rate or extent of granule cell precursor proliferation. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15157725]
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]
Any process that increases 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]
The process in which a relatively unspecialized cell acquires the specialized features of a glial cell. [GOC:go_curators, GOC:mtg_sensu]
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 stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
Any process that activates or increases the rate or extent of endothelial cell proliferation. [GOC:add]
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
The interaction of two or more cells or tissues that causes them to change their fates and specify the development of an organ. [ISBN:0878932437]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK). [PMID:9561267]
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]
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 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]
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]
Combining with the sphingolipid sphingosine-1-phosphate (S1P), and transmitting the signal across the membrane by activating an associated G-protein. [GOC:bf, PMID:12728273, Wikipedia:S1PR1]
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]
Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3. [PMID:12019236, PMID:20206496, PMID:22729156]
The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. [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]
A compact and highly condensed form of chromatin. [GOC:elh]
Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin. [GOC:BHF]
The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule. [GOC:ascb_2009, 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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. [CHEBI:33709, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The covalent transfer of a methyl group to C-5 of cytosine that contributes to the epigenetic regulation of embryonic gene expression. [GOC:go_curators, PMID:12138111]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule. [GOC:pf]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression. [GOC:dos, GOC:dph, GOC:jid, 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 involved in maintaining the methylation state of a nucleotide sequence. [PMID:11898023]
A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state. [GOC:bf]
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]
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 section of chromatin that is associated with gene promoter sequences of DNA. [PMID:19948729]
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 methyl group to a DNA molecule. [GOC:jl, ISBN:0198506732, PMID:7862522]
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide. [GOC:jl, PMID:11746232]
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]
Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine. [EC:2.1.1.37]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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]
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 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 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]
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]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
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]
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 stops, prevents or reduces the frequency, rate or extent of polyamine transmembrane transport. [GOC:TermGenie, PMID:23755272]
Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. [GOC:tb]
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]
Any process that stops or reduces the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups. [ISBN:0198506732]
The stopping, prevention or reduction of the activity of the enzyme ornithine decarboxylase. [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 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 addition of tubulin heterodimers to one or both ends of a microtubule. [GOC:ai, GOC:go_curators]
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]
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]
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]
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 multimeric protein complex that removes monoubiquitin from histone H2A. In Drosophila and mammals, the core of the complex is composed of Calypso/BAP1 and Asx/ASXL1, respectively. [PMID:20436459]
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 in the nucleus. [GOC:elh, PMID:20404130]
The biological process whose specific outcome is the progression of a lung saccule from an initial condition to its mature state. The lung saccule is the primitive gas exchange portion of the lung composed of type I and type II cells. [GOC:dph, GOC:mtg_lung]
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. [GOC:dph]
Any biological process involved in the maintenance of the steady-state number of cells within a population of cells. [GOC:isa_complete]
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]
The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components. [GOC:add, ISBN:0781735149]
The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation. [GOC:add, GOC:rl, ISBN:0781735149]
Any process that stops, prevents, or reduces the frequency, rate or extent of retinoic acid receptor signaling pathway activity. [GOC:dgh]
Any process that activates or increases the frequency, rate or extent of retinoic acid receptor signaling pathway activity. [GOC:dgh]
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 adipocyte differentiation. [GOC:go_curators]
The removal of the ubiquitin group from a monoubiquitinated histone H2A protein. [GOC:bf, PMID:18226187, PMID:20436459]
Any process that stops, prevents, or reduces the frequency, rate or extent of the peroxisome proliferator activated receptor signaling pathway. [GOC:bf]
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 retinoic acid stimulus. [GOC:sl]
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]
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 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]
The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:dph, GOC:isa_complete]
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 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 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]
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]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
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]
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 activation-induced cell death of T cells. [GOC:add, ISBN:0781765196]
Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development. [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 stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. [GOC:jl]
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 Myogenic Regulatory Factor (MRF), a member of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors. [PMID:10966875]
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 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]
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 the microtubule constituent protein gamma-tubulin. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
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]
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]
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 the plasma membrane located at the apical end of the cell. [GOC:curators]
The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium. [GOC:ecd, PMID:11839751]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
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 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 small subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
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]
A sperm-specific voltage-gated calcium channel that controls the intracellular calcium ion concentration and, thereby, the swimming behavior of sperm. Consists of a heteromeric tetramer surrounding a calcium ion- selective pore. May also contain additional auxiliary subunits. [GOC:sp, PMID:17478420, PMID:21224844, PMID:22354039]
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 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]
The process in which 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]
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 in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment. [GOC:dph, GOC:hjd, GOC:mtg_lung, PMID:1814929]
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]
Any process involved in the controlled movement of a flagellated sperm cell. [GOC:cilia, GOC:jl, GOC:krc]
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]
Enables the transmembrane transfer of a calcium ion by a channel that opens when nicotinic acid adenine dinucleotide phosphate (NAADP) has been bound by the channel complex or one of its constituent parts. [PMID:19387438, PMID:19557428]
Enables the calcium concentration-regulatable energy-independent passage of cations across a lipid bilayer down a concentration gradient. [GOC:dph, GOC:mtg_transport]
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]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [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 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 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 cell proliferation. [GOC:jl]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
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]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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]
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 membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [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 process that activates or increases the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process. [GOC:BHF]
Any process that modulates the frequency, rate or extent of protein localization to the cell surface. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process. [GOC:TermGenie, GOC:yaf]
Any process that decreases 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:dph, GOC:tb, GOC:yaf]
Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle. [GOC:BHF]
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 increases the rate, frequency, or extent of protein tyrosine kinase activity. [GOC:dph, GOC:tb]
The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland. [GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine. [GOC:ai]
Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine. [GOC:ai]
The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder. [GOC:dgh, 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 activates or increases the frequency, rate or extent of mitosis. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of MAP kinase activity. [GOC:dph, GOC:go_curators]
Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb]
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. [GOC:jl]
Any process that increases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus. [GOC:BHF]
The process that activates or increases the rate or extent of granule cell precursor proliferation. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15157725]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine. [GOC:dph, GOC:tb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The directed movement of dimerized STAT (Signal Transducers and Activators of Transcription) proteins into the nucleus following activation by members of the janus activated kinase (JAK) family of tyrosine kinases. [GOC:jl, PMID:12039028]
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]
Any process that activates or increases the frequency, rate or extent of receptor internalization. [GOC:hjd]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
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]
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 epidermal growth factor receptor. [GOC:ai]
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]
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. [GOC:add, ISBN:0781735149]
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 B cell activation. [GOC:ai]
A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell. [GOC:add]
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]
Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes. [GOC:add, ISBN:0781735149]
The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis. [GOC:curators, ISBN:0781735149]
The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell. [GOC:curators, ISBN:0781735149]
Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule. [GOC:BHF, GOC:vk]
Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. [GOC:jl, ISBN:0198506732, ISBN:0721662544]
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]
The trimethylation of the N-terminal serine of proteins to form the derivative N,N,N-trimethylserine. [PMID:20668449]
The dimethylation of the N-terminal serine of proteins to form the derivative N,N-dimethylserine. [PMID:20668449]
The methylation of the N-terminal serine of proteins. [PMID:20668449]
The methylation of the N-terminal proline of proteins. [PMID:20668449, RESID:AA0419]
The methylation of the N-terminal proline of proteins to form the derivative N,N-dimethyl-L-proline. [RESID:AA0066]
The methylation of the N-terminal glycine of proteins to form the derivative N-methylglycine. [RESID:AA0063]
The trimethylation of the N-terminal alanine of proteins to form the derivative peptidyl-N,N,N-trimethyl-L-alanine. [RESID:AA0062]
The methylation of the N-terminal alanine of proteins. [RESID:AA0061, RESID:AA0062]
The modification of histones by addition of methyl groups. [GOC:ai]
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart. [GOC:go_curators, GOC:mah]
The methylation of the N-terminal amino acid of a protein. [GOC:ai]
Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to the alpha-amino group of the N-terminal amino or imino acid residue of a protein substrate. For example, yeast Tae1p and mammalian family member METTL11A preferentially modify the N-terminal residue of substrates with the N-terminal sequence X-Pro-Lys, where X can be Pro, Ala, or Ser. [PMID:20481588]
Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue. [EC:2.1.1.43]
Catalysis of the transfer of a methyl group (CH3-) to a protein. [GOC:jl, ISBN:0198506732]
Catalysis of the transfer of a methyl group to an acceptor molecule. [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]
A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan. [GOC:pr, RESID:AA0151, RESID:AA0156, RESID:AA0327]
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]
Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor). [GOC:jl]
Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
Catalysis of the transfer of an N-acetylglucosaminyl residue from UDP-N-acetyl-glucosamine to a sugar. [ISBN:0198506732]
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]
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 modulates the frequency, rate or extent of multicellular organismal development. [GOC:obol]
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]
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 modulates the frequency, rate or extent of mammary gland epithelial cell proliferation. [GOC:mah]
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]
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]
The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline. [GOC:dph, ISBN:0878932437]
An acute behavioral change resulting from a perceived external threat. [GOC:dph, PMID:9920659]
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]
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 cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
Any microtubule in the cytoplasm of a cell. [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 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 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 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]
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]
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 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 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 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]
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]
A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. [GOC:mah, ISBN:0198506732, PMID:10666339]
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 change in form that occurs when an epithelial cell progresses from its initial formation to its mature state. [GOC:ascb_2009, GOC:dph, GOC:tb]
The process whose specific outcome is the progression of a keratinocyte over time, from its formation to the mature structure. [GOC:dph]
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]
Any process that stops, prevents or reduces the rate or extent of T cell proliferation. [GOC:jl]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production. [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 ribonucleoprotein granule located in the cytoplasm. [GOC:bf, GOC:PARL, PMID:15121898]
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 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]
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 activates or increases the frequency, rate or extent of transcription of nuclear large rRNA transcript from RNA polymerase I promoter. [GOC:sart, 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 epidermal growth factor stimulus. [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]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end. [GOC:jl, SO:0000624]
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]
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 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 the removal of one or more acetyl groups. [GOC:BHF, GOC:rl]
The modification of histones by removal of acetyl groups. [GOC:ai]
The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups. [GOC:mah, GOC:vw]
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]
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]
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: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes. [EC:3.5.1.98, PMID:9893272]
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/]
An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins. [PMID:10589671, PMID:11743021, PMID:17289569]
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 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]
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. [GOC:elh, PMID:20404130]
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 modification of histone H4 by the removal of one or more acetyl groups. [GOC:BHF, GOC:rl]
Any process that decreases the rate, frequency, or extent of the androgen receptor signaling pathway. [GOC:dph]
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 cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process in which a host organism stops, prevents, or reduces the frequency, rate or extent of viral transcription. [GOC:jl]
Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors. [GOC:jl, PMID:12042764]
Any process that increases the frequency or rate of receptor biosynthesis. Receptor biosynthesis is the collection of chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:BHF, GOC:tb]
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 that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. [GOC:ai]
Repression of transcription by methylation of DNA, leading to the formation of heterochromatin. [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]
Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription. [GOC:mah, GOC:txnOH]
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 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]
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 the enzyme histone deacetylase. [GOC:jl]
Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription. [GOC:mah, GOC:txnOH]
Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate. [GOC:mah]
Interacting selectively and non-covalently with the DNA portion of a nucleosome. [GOC:mah]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
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 an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription. [GOC:txnOH]
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II. [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 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 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 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 complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60). [GOC:ecd, PMID:10966108, PMID:14966270]
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]
The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. [GOC:mah, 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 modification of histone H2A by the addition of an acetyl group. [GOC:jl]
The modification of histone H4 by the addition of an acetyl group. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. [GOC:jl]
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 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 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 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]
Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription. [GOC:txnOH]
A protein complex that functions in the retrotranslocation step of ERAD (ER-associated protein degradation), and includes at its core Derlin-1 oligomers forming a retrotranslocation channel. [GOC:bf, GOC:PARL, PMID:15215856, PMID:16186510]
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 modulates the frequency, rate or extent of autophagosome assembly. [GOC:autophagy, GOC:BHF]
The chemical reactions and pathways resulting in the breakdown of misfolded proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation. [GOC:mah, GOC:vw, PMID:14607247, PMID:19520858]
A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation. [GOC:cvs, PMID:15556404]
A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair. [GOC:mah, PMID:15556404]
The chemical reactions and pathways resulting in the breakdown of a protein by individual cells. [GOC:jl]
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 series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome. [GOC:bf, GOC:PARL]
Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation. [GOC:mah]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
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 a stimulus from a bacterium. [GOC:hb]
Any ubiquitin protein ligase activity that is involved in the ERAD pathway (the targeting of endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome). [GO_REF:0000061, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:23990462]
Interacting selectively and non-covalently with a ubiquitin-like protein conjugating enzyme such as ubiquitin conjugating enzyme. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
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]
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]
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 directed movement of ferric iron (Fe(III) or Fe3+) ions 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 iron ions at the level of a cell. [GOC:ai, GOC:mah]
The directed movement of iron (Fe) 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 ferric iron (Fe(III) or Fe3+) ions from one side of a membrane to the other. [ISBN:0198506732]
Interacting selectively and non-covalently with ferric iron, Fe(III). [GOC:ai]
A protein complex containing at least HFE and a transferrin receptor (either TFR1/TFRC or TFR2), proposed to play a role in the sensing of transferrin-bound Fe (Fe2-Tf) on the plasma membrane to regulate hepcidin transcription. [GOC:BHF, GOC:kom, PMID:25147378]
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]
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]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
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]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its external surface, but not integrated into the hydrophobic region. [GOC:dos, 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]
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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
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]
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 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 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]
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 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 ferrous iron (Fe(II) or Fe2+) ions from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis. [GOC:mah, PMID:8321236]
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 iron ion stimulus. [GOC:mah]
Any process that activates or increases 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, GOC:tb]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
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]
A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function. [GOC:add, GOC:dph, GOC:tb, PMID:15365173, PMID:15365178]
Interacting selectively and non-covalently with the transferrin receptor. [PMID:9819414, PMID:pm]
Interacting selectively and non-covalently with ferrous iron, Fe(II). [GOC:ai]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Interacting selectively and non-covalently with the signal recognition particle. [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 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 ion channel complex through which calcium ions pass. [GOC:mah]
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 protein complex that has protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic, scaffolding, and regulatory subunits. The catalytic and scaffolding subunits form the core enzyme, and the holoenzyme also includes the regulatory subunit. [GOC:mah, ISBN:0198547684, PMID:17245430]
Any process that modulates the frequency, rate or extent of phosphoprotein phosphatase activity, the catalysis of the hydrolysis of phosphate from a phosphoprotein. [GOC:jp, PMID:11724821]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process the stops, prevents, or reduces the frequency, rate or extent of removal of phosphate groups from a protein. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein. [GOC:bf]
Any process that activates or increases the activity of a phosphoprotein phosphatase. [GOC:mah]
Any process that stops or reduces the activity of a phosphoprotein phosphatase. [GOC:mah]
A process resulting in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle in the nucleus. The process occurs during a mitotic cell cycle and takes place at the cellular level. [GOC:mah]
The modification of a protein by cis-trans isomerization of a proline residue. [GOC:krc, PMID:16959570]
Interacting selectively and non-covalently with the enzyme protein phosphatase 2A. [GOC:ai]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Modulates the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule. [GOC:ai]
Increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule. [GOC:ai]
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 the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. [ISBN:0198506732]
Increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a tyrosyl phenolic group of a protein. [GOC:ai, 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: peptidyl-proline (omega=180) = peptidyl-proline (omega=0). [EC:5.2.1.8]
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]
Polarized accumulation of cytoskeletal proteins (including F-actin) and regulatory proteins in a cell. An example of this is the actin cap found in Saccharomyces cerevisiae. [GOC:mah, ISBN:10652251]
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]
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 frequency, rate or extent of Arp2/3 complex-mediated actin nucleation. [PMID:21454476]
Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte migration. [GOC:mah]
Any process that stops, prevents or reduces the frequency, rate or extent of membrane tubulation. [GO_REF:0000058, GOC:pm, GOC:TermGenie, PMID:18388313]
The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission. [GOC:dph]
Any process in which is the spindle is transported to, and/or maintained in, a specific location. [GOC:ai]
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 that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. [GOC:dph, GOC:mah, 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 comprising actin filaments and their associated proteins. [GOC:dph, GOC:jl, 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 stimulus from a bacterium. [GOC:hb]
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 monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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]
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. [GOC:mah, GOC:pz]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The directed movement of a pre-mRNA splicing factor from the cytoplasm into the nucleus, across the nuclear membrane. [GOC:bf]
The directed movement of a protein from the cytoplasm to the nucleus. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [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 a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus. [GOC:ai]
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]
A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state. [GOC:bf]
A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state. [GOC:bf]
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]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule. [GOC:mah]
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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the reaction: S-adenosyl-L-methionine + tRNA containing guanine = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine. [EC:2.1.1.32]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [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]
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 guanine in a tRNA is methylated at the N2 position of guanine. [ISBN:155581073X, ISBN:1555811337]
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 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 into a cell or organelle. [GOC:sm]
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 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 transmembrane transfer of a potassium ion by an inwardly-rectifying voltage-gated channel. An inwardly rectifying current-voltage relation is one where at any given driving force the inward flow of K+ ions exceeds the outward flow for the opposite driving force. The inward-rectification is due to a voltage-dependent block of the channel pore by a specific ligand or ligands, and as a result the macroscopic conductance depends on the difference between membrane voltage and the K+ equilibrium potential rather than on membrane voltage itself. [GOC:cb, GOC:mah, PMID:14977398]
A process in which a potassium ion is transported from one side of a membrane to the other. [GOC:mah]
The larger subcomplex of the intraciliary transport particle; characterized complexes have molecular weights around 550 kDa. [GOC:cilia, GOC:kmv, PMID:14570576, PMID:19253336]
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]
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 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 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 stops, prevents or reduces the rate or extent of epithelial cell proliferation. [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]
The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. [GOC:cilia, GOC:kmv, PMID:17981739, PMID:18180368, PMID:22869374, Reactome:R-HSA-5620924.2]
The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. [GOC:bf, GOC:cilia, Reactome:R-HSA-5620924.2]
Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin. [GOC:add]
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]
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 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 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 the microtubule constituent protein beta-tubulin. [GOC:krc]
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 region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end. [ISBN:0321204131]
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]
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 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]
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 stops, prevents or reduces the frequency, rate or extent of autophagosome assembly. [GO_REF:0000058, GOC:als, GOC:autophagy, GOC:TermGenie, PMID:21975012]
The process in which the anatomical structures of a mitochondrion are generated and organized. [GOC:mah]
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]
Any process that activates, maintains or increases the rate of skeletal muscle growth. [GOC:lm, PMID:15726494, PMID:15907921]
Any process that establishes the spatial arrangement of mitochondria between and within cells. [GOC:jid]
The process of removing one or more phosphate groups from a phosphatidylinositol. [ISBN:0198506732]
The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state. [GOC:mah, PMID:3091429, PMID:7781901]
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 modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. [GOC:jl, GOC:mah]
The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine. [GOC:bf]
Any process that stops, prevents, or reduces 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]
Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling. [GOC:mah]
The process of removing one or more phosphoric (ester or anhydride) residues from a molecule. [ISBN:0198506732]
The directed movement of substances from endosomes to lysosomes. [GOC:ai, ISBN:0716731363]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate + 2 H+. [MetaCyc:RXN-10958, PMID:19901554]
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 an intermediate filament, a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher 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. [ISBN:0198506732]
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 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]
Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O = 1-phosphatidyl-1D-myo-inositol + phosphate. [EC:3.1.3.64]
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 activity of a GTPase. [GOC:jl, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. [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]
Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases. [GOC:ebc, PMID:11702775]
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 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]
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]
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]
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 a calcium ion stimulus. [GOC:mah]
A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair. [GOC:jc, PMID:16460914, PR:000002082, Reactome:REACT_115755.1]
Any process that activates or increases the frequency, rate or extent of cell migration. [GOC:go_curators]
The process of introducing a phosphate group on to a protein. [GOC:hb]
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 a receptor that possesses protein tyrosine kinase activity. [GOC:mah]
Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium. [GOC:jl]
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 an RNA molecule or a portion thereof. [GOC:mah]
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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
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 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 process that activates or increases the frequency, rate, or extent of interleukin-6 production. [GOC:mah]
Any process that modulates the frequency, rate, or extent of tumor necrosis factor production. [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]
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. [GOC:dph]
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 a synapse that is part of the post-synaptic cell. [GOC:dos]
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]
Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway. [GOC:mtg_apoptosis]
A process that causes a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential. [GOC:dph, GOC:ef]
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 alpha-beta T cell activation. [GOC:ai]
The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue. [GOC:jl, GOC:pr, ISBN:01928006X]
Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA). [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate). [GOC:mah]
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]
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 molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation of adenylyl cyclase activity and a subsequent increase 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 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 or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine. [CHEBI:2679, GOC:dph, GOC:ef]
The series of molecular signals generated as a consequence of a receptor binding to extracellular adenosine and transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. [GOC:dph]
The process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine. [GOC:dph]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
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]
Combining with adenosine 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, GOC:mah, PMID:9755289]
A protein complex that forms a subcomplex of the 90S preribosome and is required for the subsequent assembly of the rest of the preribosome. In S. cerevisiae, it is composed of Utp5p, Utp4p, Nan1p, Utp8p, Utp9p, Utp10 and Utp15p. [GOC:krc, GOC:mah, GOC:vw, PMID:17515605]
A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins. [GOC:krc, GOC:vw, PMID:12068309, PMID:12957375, PMID:15120992, PMID:15590835]
A large ribonucleoprotein complex considered to be the earliest preribosomal complex. In S. cerevisiae, it has a size of 90S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins. [GOC:krc, GOC:vw, PMID:12150911, PMID:12957375, PMID:15120992]
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]
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 transcription from an RNA polymerase I promoter. [GOC:go_curators, GOC:txnOH]
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]
Interacting selectively and non-covalently with small nucleolar RNA. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
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]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, ISBN:0815316194]
A myosin complex containing two class II myosin heavy chains, two myosin essential light chains and two myosin regulatory light chains. Also known as classical myosin or conventional myosin, the myosin II class includes the major muscle myosin of vertebrate and invertebrate muscle, and is characterized by alpha-helical coiled coil tails that self assemble to form a variety of filament structures. [http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html, ISBN:96235764]
A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber. [PMID:16651381]
The adhesion of one platelet to one or more other platelets via adhesion molecules. [GOC:BHF, GOC:vk]
Interacting selectively and non-covalently with a heavy chain of a myosin complex. [GOC:mah]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
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]
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 any cellular process that depends upon or alters the microtubule cytoskeleton. [GOC:mah]
The large 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 chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. [GOC:hjd]
The action of a molecule that contributes to the structural integrity of the ribosome. [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]
The chemical reactions and pathways involving carnitine, where metabolism is linked to CoA. [GOC:go_curators]
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]
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: acetyl-CoA + carnitine = (R)-O-acetylcarnitine + CoA. [EC:2.3.1.7, RHEA:21139]
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 organ system process carried out by any of the organs or tissues of neurological system. [GOC:ai, GOC:mtg_cardio]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. [GOC:jl]
Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. [GOC:BHF, GOC:tb]
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]
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]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
A proteasome specifically found in mammalian testis. Contains the proteasome activator PA200 in the regulatory particle, and beta1i, beta2i, beta5i and/or alpha4s in the core (20S) subunit. Beta1i, beta2i and beta5i are inducible catalytic subunits, closely related to beta1, beta2 and beta5. Alpha4s is a sperm-specific 20S subunit, but unlike other alternative 20S subunits alpha4s lies in the outer alpha-ring and lacks catalytic activity. [GOC:sp, PMID:23706739]
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 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]
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]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. [http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
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 fatty acid oxidation process in which the methyl group at the end of the fatty acid molecule (the omega carbon) is first oxidized to a hydroxyl group, then to an oxo group, and finally to a carboxyl group. The long chain dicarboxylates derived from omega-oxidation then enter the beta-oxidation pathway for further degradation. [MetaCyc:PWY-2724, PMID:16404574]
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 lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The lipid bilayer surrounding any of the compartments of the Golgi apparatus. [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 aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid. [GOC:go_curators]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and molecular oxygen is incorporated into a donor. [GOC:mah]
Catalysis of the reaction: 4-hydroxyphenylpyruvate + O2 = homogentisate + CO2. [EC:1.13.11.27]
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]
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. [GOC:mah, GOC:pz]
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 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]
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 lipid bilayer surrounding a late endosome. [GOC:pz]
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 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]
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]
An endosomal sorting complex required for transport and functions downstream of ESCRT I complex. It consists of the class E vacuolar protein sorting (Vps) proteins and is required for the membrane recruitment of ESCRT III complex and binds to ubiquitinated cargoes. [GOC:rb, PMID:12892785, PMID:12900393]
The process of directing proteins towards the vacuole using signals contained within the protein, occurring that contributes to protein catabolism via the multivesicular body (MVB) pathway. [GOC:jl, PMID:11511343]
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 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 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]
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 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 lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink. [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 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]
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]
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 collagen heterotrimer containing type XI alpha chains in alpha1(XI)alpha2(XI)alpha3(XI) trimers; type XI collagen triple helices associate to form fibrils. [ISBN:0721639976]
A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911]
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 in which the anatomical structures of cardiac ventricle muscle is generated and organized. [GOC:devbiol]
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 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 in which the anatomical structures of the skeleton are generated and organized. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb]
The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113]
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 process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force. [GOC:yaf, PMID:21412429, UBERON:0000043]
The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo. [CL:0000223, GOC:yaf, PMID:17624332]
Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix. [GOC:mah, ISBN:0815316194]
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 chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans. [GOC:mah, ISBN:0198506732]
The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:dph, GOC:isa_complete]
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 condensation of mesenchymal cells that have been committed to differentiate into chondrocytes. [ISBN:0878932437]
The action of a molecule that contributes to the structural integrity of the extracellular matrix. [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]
Any process that prevents the activation of an inactive cysteine-type endopeptidase involved in an apoptotic process. [GOC:mtg_apoptosis, PMID:11943137]
Any process that activates or increases the frequency, rate or extent of protein linear polyubiquitination. [GOC:TermGenie, PMID:21931591]
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 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 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 activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein. [GOC:mah]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
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]
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 an identical protein or proteins. [GOC:jl]
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 cohesin complex that mediates sister chromatid cohesion during mitosis; has a subunit composition distinct from that of the meiotic cohesin complex. [GOC:mah, PMID:12750522]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. [GOC:cjm, GOC:elh, GOC:kmv, GOC:pr]
The cell cycle process in which centromeres of sister chromatids are joined during meiosis. [PMID:14730319, PMID:16325576]
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]
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 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]
Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. [GOC:mah]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
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]
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. [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 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]
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]
Enables the directed movement of proteins into, out of or within a cell, or between cells. [ISBN:0198506732]
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 any metal ion. [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 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 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]
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]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, 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]
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 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 the assembly of actin filament bundles. [GOC:mah]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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 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 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 a nicotinateacetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:obol]
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, sodium-independent, 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]
The directed movement of urate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:krc]
The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage. [GOC:krc]
Enables the directed movement of nicotinate into, out of or within a cell, or between cells. [GOC:tb]
Enables the transfer of a substance from one side of a membrane to the other. [GOC:mtg_transport, ISBN:0815340729]
Catalysis of the transfer of organic anions from one side of a membrane to the other, in a sodium independent manner. [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: inorganic anion A(out) + inorganic anion B(in) = inorganic anion A(in) + inorganic anion B(out). [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]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
The chemical reactions and pathways resulting in the formation of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions. [CHEBI:38290, GOC:ma, ISBN:0198547684]
Binds to and modulates the activity of an enzyme. [GOC:dph, GOC:mah, GOC:tb]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Catalysis of the reaction: D-glucono-1,5-lactone + H2O = D-gluconate. [EC:3.1.1.17]
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]
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]
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 modulates the frequency, rate or extent of mitochondrion degradation (mitophagy). [GO_REF:0000058, GOC:autophagy, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24600391]
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]
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]
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 ribonucleoprotein complex that contains small nuclear RNA U1. [GOC:krc, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell differentiation. [CL:0000192, GOC:ai]
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 an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop. [GOC:sart, PMID:16568238, PMID:20455544]
Interacting selectively and non-covalently with the U1 small nuclear RNA (U1 snRNA). [GOC:mah]
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]
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 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 spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation. [GOC:ab, GOC:krc, GOC:mah, PMID:17332742, PMID:19239890]
A ribonucleoprotein complex that contains small nuclear RNA U2. [GOC:krc, GOC:mah]
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]
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 a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide. [GOC:mah]
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 any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
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]
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 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]
A protein complex comprising nitric oxide synthase 2 and CD74. This stable complex formation is thought to prevent CD74 degradation by caspases. [GOC:BHF, PMID:18003616]
A protein complex that binds macrophage migration inhibitory factor. Comprises CD74 and CD44 cell surface proteins. [GOC:BHF, PMID:12782713, PMID:17045821]
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]
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 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 closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. [GOC:mtg_sensu, ISBN:0198506732]
A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm. [PMID:11566881, PMID:16533950]
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]
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]
Any process that activates or increases the frequency, rate or extent of chemokine (C-X-C motif) ligand 2 production. [GOC:BHF, GOC:mah]
Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator. [GOC:TermGenie, PMID:17719541]
Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. [GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:mah]
Any process that increases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:dph, GOC:tb]
The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release. [GOC:rb]
Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells. [GOC:jid]
Any process that activates or increases the frequency, rate or extent of T cell differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation. [GOC:go_curators]
The process of elimination of immature T cells in the thymus which react strongly with self-antigens. [ISBN:0781735149, PMID:12414722]
The process of sparing immature T cells in the thymus which react with self-MHC protein complexes with low affinity levels from apoptotic death. [ISBN:0781735149, PMID:12414722]
Any process that stops, prevents, or reduces the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage. [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]
A series of molecular signals initiated by the binding of macrophage migration inhibitory factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:BHF, GOC:signaling, PMID:12782713, PMID:19413900]
Any process that activates or increases the rate or extent of B cell proliferation. [GOC:mah]
The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein. [GOC:add, ISBN:0781735149, PMID:15771591]
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]
An immune response mediated by immunoglobulins, whether cell-bound or in solution. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
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]
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]
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]
Any process that stops, prevents, or reduces the frequency, rate, or extent of mature B cell apoptotic process. [GOC:add, GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate, or extent of a type 2 immune response. [GOC:add]
Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. [GOC:add]
Any process that activates or increases the frequency, rate, or extent of dendritic cell antigen processing and presentation. [GOC:add]
Any process that activates or increases the frequency, rate or extent of a cytokine mediated signaling pathway. [GOC:hjd]
The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring. [GOC:ai]
Interacting selectively and non-covalently with the enzyme nitric-oxide synthase. [GOC:ai]
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding. [GOC:mtg_cambridge_2009]
Interacting selectively and non-covalently with the antigen binding groove of major histocompatibility complex class II molecules. [GOC:jl]
Interacting selectively and non-covalently with major histocompatibility complex class II molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation. [GOC:jl]
Interacting selectively and non-covalently with the cytokine, macrophage migration inhibitory factor. [GOC:BHF, PMID:19601712]
Interacting selectively and non-covalently with the class II major histocompatibility complex. [GOC:mtg_signal, GOC:vw]
Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity. [GOC:ai, GOC:bf, ISBN:0198599471]
Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:add, GOC:mah]
Interacting selectively and non-covalently with beta-amyloid peptide/protein and/or its precursor. [GOC:hjd]
The transfer, from NAD, of ADP-ribose to protein amino acids. [GOC:pr, RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295]
The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix. [GOC:elh]
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: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor. [EC:2.4.2.30]
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]
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 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]
Any process in which a protein is transported to, or maintained at, a region of a chromosome at which a DNA double-strand break has occurred. [GOC:mah, PMID:23080121]
Any process that modulates the rate, frequency or extent of the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle. [GOC:ascb_2009, GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase. [GOC:ai]
The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair. [GOC:ai]
The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork. [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]
Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m). [EC:6.5.1.1]
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 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 the phospholipid derivative lysophosphatidic acid, and transmitting the signal across the membrane by activating an associated G-protein. [CHEBI:52288, GOC:bf, GOC:mah, PMID:15755723]
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 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]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
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 vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
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 the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts. [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 activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade. [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 Rho protein signal transduction. [GOC:bf]
The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. [GOC:mah, GOC:mtg_apoptosis, http://en.wikipedia.org/wiki/Bleb_(cell_biology), PMID:12083798, PMID:16624291]
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 modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand. [GOC:dph, GOC:mah, GOC:tb, PMID:8280098]
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]
The initiation of the activity of the inactive enzyme MAP kinase (MAPK). [PMID:9561267]
Interacting selectively and non-covalently with lysophosphatidic acid (LPA), a phospholipid derivative that acts as a potent mitogen due to its activation of high-affinity G-protein-coupled receptors. [CHEBI:52288]
Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins. [GOC:go_curators, Pfam:PF00595]
The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step. [GOC:ai, GOC:dph, PMID:2198020]
Catalysis of the reaction: (S)-(2-hydroxyacyl)glutathione + H2O = glutathione + a 2-hydroxy carboxylate. [EC:3.1.2.6]
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 mRNA processing, those processes involved in the conversion of a primary mRNA transcript into a mature mRNA prior to its translation into polypeptide. [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]
The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. [CHEBI:24621, GOC:jl]
The increase in size or mass of an entire organism, a part of an organism or a cell. [GOC:bf, GOC:ma]
Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription). [GOC:mah, GOC:signaling]
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 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 an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with double-stranded DNA. [GOC:elh, GOC:vw]
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 any nucleic acid. [GOC:jl]
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 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 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 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 decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. [GOC:BHF, GOC:dph, GOC:tb]
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]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
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 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]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. [GOC:krc]
The controlled release of lysosomal enzymes by a cell. [GOC:mah]
The directed movement of mannose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Mannose is the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins. [GOC:ai]
Interacting selectively and non-covalently with a retromer complex. [GO_REF:000102, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:27385586]
Enables the transfer of mannose from one side of the membrane to the other. Mannose is the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins. [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans. [CHEBI:37684, GOC:jl, ISBN:0192800981]
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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
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 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 chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. [CHEBI:16670, 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 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]
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]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [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]
A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan. [GOC:pr, RESID:AA0151, RESID:AA0156, RESID:AA0327]
Catalysis of the reaction: dolichyl diphosphate + H2O = dolichyl phosphate + phosphate. [EC:3.6.1.43, MetaCyc:DOLICHYLDIPHOSPHATASE-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]
Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + protein = UDP + 4-N-(N-acetyl-D-glucosaminyl)-protein. [EC:2.4.1.94]
Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan. [GOC:pr, ISBN:0879695595, RESID:AA0153, RESID:AA0154, RESID:AA0155, RESID:AA0157, RESID:AA0212]
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 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 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 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 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]
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]
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]
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 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 calcium ion stimulus. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of keratinocyte migration. [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 hydrogen peroxide (H2O2) stimulus. [GOC:jl]
The change in morphology and behavior of a monocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor. [GOC:mgi_curators, ISBN:0781735149]
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 tumor necrosis factor stimulus. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of macrophage fusion. [GOC:mah]
The attachment of one cell to another cell via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits. [GOC:add, PMID:12213832, PMID:14754902]
Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin. [GOC:add]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits. [GOC:add, PMID:12213832, PMID:14754902]
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 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 manganese ion stimulus. [GOC:sm]
A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:BHF, GOC:mah, GOC:signaling]
The binding of a cell to the extracellular matrix via adhesion molecules. [GOC:hb]
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]
The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain). [GOC:jl, http://www.copewithcytokines.de/]
The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK). [PMID:9561267]
Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells. [GOC:ecd]
Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins. [GOC:go_curators, Pfam:PF00018]
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]
Interacting selectively and non-covalently with an integrin. [GOC:ceb]
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]
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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
Any process that activates or increases the frequency, rate or extent of interleukin-1-mediated signaling pathway. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of neutrophil extravasation. [GOC:BHF, 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 an interleukin-1 stimulus. [GOC:BHF, 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 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]
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]
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 interleukin-1. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with the platelet-derived growth factor receptor. [GOC:ai]
Combining with interleukin-1 to initiate a change in cell activity via signaling pathways and mediated by adaptor proteins. [PMID:15062641, PMID:18613828]
Combining with interleukin-1 to initiate a change in cell activity. Interleukin-1 is produced mainly by activated macrophages and is involved in the inflammatory response. [GOC:jl]
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 any protease or peptidase. [GOC:hjd]
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 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 protein monoubiquitination. [GOC:TermGenie, PMID:21931591]
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 activates or increases the rate or extent of epithelial cell proliferation. [GOC:ai]
Any biological process involved in the maintenance of the steady-state number of cells within a population of cells. [GOC:isa_complete]
The process in which the anatomical structures of the skeleton are generated and organized. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb]
Development, taking place during the embryonic phase, 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:jid]
The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue. [GOC:jl, UBERON:0002097]
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 removal of one or more ubiquitin groups from a protein. [GOC:ai]
The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure. [GOC:jid]
The union of male and female gametes to form a zygote. [GOC:ems, GOC:mtg_sensu]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
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 error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule. [GOC:elh, PMID:10357855]
Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area. [GOC:cilia, GOC:krc, PMID:22653444]
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]
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]
An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer. [EC:2.7.11.11, 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]
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 cAMP-dependent protein kinase activity. [GOC:obol]
Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. [ISBN:0582227089, ISBN:0721662544]
The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. [ISBN:0198547684]
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 one or both of the catalytic subunits of protein kinase A. [GOC:mah]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate). [GOC:ai]
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]
Modulation of the activity of the enzyme cAMP-dependent protein kinase. [GOC:ai]
Stops, prevents or reduces the activity of a cAMP-dependent protein kinase. [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 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]
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. [GOC:add, ISBN:0781735149]
Any process that modulates the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria. [GOC:ai, GOC:tb]
A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell. [GOC:add]
A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell. [GOC:add]
Any process that modulates the frequency, rate or extent of MAP kinase activity. [GOC:dph, GOC:go_curators]
Any process that modulates I-kappaB kinase/NF-kappaB signaling. [GOC:jl, PMID:12773372]
Any process that modulates the frequency, rate or extent of the 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 modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade. [GOC:ef]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Disassembly of a spliceosomal complex with the ATP-dependent release of the product RNAs, one of which is composed of the joined exons. In cis splicing, the other product is the excised sequence, often a single intron, in a lariat structure. [GOC:krc, ISBN:0879695897]
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 component of the cell outer 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:go_curators, GOC:mtg_sensu]
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. [GOC:dph]
Merging of two or more mitochondria within a cell to form a single compartment. [PMID:11038192]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [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]
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 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 prostaglandin E (PGE(2)) to initiate a change in cell activity. [ISBN:0198506732]
Combining with a prostaglandin (PG) to initiate a change in cell activity. [ISBN:0198506732]
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 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 cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. [GOC:BHF, GOC:dph, GOC:tb]
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 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 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 a sequence of DNA that is in the transcription regulatory 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: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]
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]
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 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 pheromone stimulus. [GOC:jl]
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 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]
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 whose specific outcome is the progression of the lacrimal gland over time, from its formation to the mature structure. The lacrimal gland produces secretions that lubricate and protect the cornea of the eye. [GOC:ln]
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 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 prevents the activation of an inactive cysteine-type endopeptidase involved in an apoptotic process. [GOC:mtg_apoptosis, PMID:11943137]
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 modulates 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 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 toll-like receptor signaling pathway. [GOC:add, PMID:16551253, PMID:17328678]
Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein. [GOC:mah]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
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]
Interacting selectively and non-covalently with any metal ion. [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]
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 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 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 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 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]
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]
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 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 an interferon-beta stimulus. Interferon-beta is a type I interferon. [GOC:sl, PR:000024939]
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 in which a secondary structure of RNA are broken or 'melted'. [PMID:17169986]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
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 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]
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]
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 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 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]
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/]
Interacting selectively and non-covalently with hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine. [CHEBI:16336, GOC:jl]
The action of a molecule that contributes to the structural integrity of the extracellular matrix. [GOC:mah]
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. [ISBN:0198547684]
The process in which one or more ubiquitin groups are added to a protein. [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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. [GOC:hb]
The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway. [PMID:10197977, PMID:11900249]
Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits. [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 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]
Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:add, GOC:mah]
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 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 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]
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]
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]
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 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 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 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]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes. [GOC:dph, GOC:jl, GOC:mah]
The process that results in the return of receptor molecules to an active state and an active cellular location after they have been stimulated by a ligand. An active state is when the receptor is ready to receive a signal. [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 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 nucleoside across a membrane. [GOC:pr, GOC:TermGenie]
The directed movement of a nucleoside, a nucleobase linked to either beta-D-ribofuranose (ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleotide), 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 nucleoside, a nucleobase linked to either beta-D-ribofuranose (ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleotide) from one side of a membrane to the other. [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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). [GOC:mah]
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 ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [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 acts as an aryl hydrocarbon (Ah) receptor. Cytosolic and nuclear Ah receptor complexes have different subunit composition, but both contain the ligand-binding subunit AhR. [GOC:mah, PMID:7598497]
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]
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]
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 protein localization to the cell surface. [GOC:obol]
The aggregation, arrangement and bonding together of a set of components to form a telomerase holoenzyme complex. [GO_REF:0000079, GOC:TermGenie, PMID:26305931]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. [GOC:pr]
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-4 stimulus. [GOC:mah]
Any process that modulates 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 modulates 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 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 modulates the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of cell differentiation. [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 activates or increases the activity of a phosphoprotein phosphatase. [GOC:mah]
Any process that stops, prevents, or reduces 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]
Any process that modulates the frequency, rate or extent of the addition of ubiquitin groups to a protein. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity. [GOC:go_curators]
The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection. [GOC:bf, GOC:jl, UniProtKB-KW:KW-1161, VZ:956]
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 organic substance stimulus. [GOC:sm]
The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase. [GOC:elh]
The 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]
Interacting selectively and non-covalently with a histone methyltransferase enzyme. [GOC:ame, GOC:BHF, PMID:19486527]
Interacting selectively and non-covalently with a DNA polymerase. [GOC:BHF, GOC:mah]
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 cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with the enzyme histone deacetylase. [GOC:jl]
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 the class II major histocompatibility complex. [GOC:mtg_signal, GOC:vw]
Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group. [GOC:jl]
Modulates the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
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]
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 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 lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
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 (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 I-kappaB kinase/NF-kappaB signaling. [GOC:jl]
Any process that stops, prevents, or reduces the frequency, rate or extent of the 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 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 modulates the frequency, rate, or extent of production of a cytokine. [GOC:add, ISBN:0781735149]
Interacting selectively and non-covalently with a WW domain of a protein, a small module composed of 40 amino acids and plays a role in mediating protein-protein interactions via proline-rich regions. [PMID:14531730]
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 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/]
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]
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 chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
Any process that modulates the frequency, rate or extent of transcription regulatory region DNA binding. [GOC:obol]
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 the JAK-STAT signaling pathway. [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 modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone. [GOC:se]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups. [GOC:mah, GOC:vw]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
Repression of transcription of telomeric DNA by altering the structure of chromatin. [PMID:10219245]
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 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]
Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue. [EC:2.1.1.43]
Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). This reaction is the addition of a methyl group onto lysine at position 79 of the histone H3 protein. [GOC:mah, PMID:15371351]
Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives. [EC:2.1.1.43, RESID:AA0074, RESID:AA0075, RESID:AA0076]
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 methyl group to an acceptor molecule. [ISBN:0198506732]
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 formation of tooth enamel, occurring in two stages: secretory stage and maturation stage. [GOC:cjm, GOC:sl, PMID:10206335, PMID:21196346]
Any process that activates or increases the frequency, rate or extent of enamel mineralization, the deposition of calcium salts in tooth enamel. [GOC:BHF, GOC:mah]
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 a relatively unspecialized cell acquires specialized features of an ameloblast, a cylindrical epithelial cell in the innermost layer of the enamel organ. [CL:0000059]
Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized. [GOC:isa_complete]
The action of a molecule that contributes to the structural integrity of tooth enamel. [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 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 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 transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans. [GOC:krc, PMID:11979277]
Any process that activates or increases the activity of a helicase. [GOC:ai]
Any process that activates or increases the rate of ATP hydrolysis by an ATPase. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the covalent addition of methyl groups to histones. [GOC:mah]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The directed movement of mRNA from the nucleus to the cytoplasm. [GOC:ma]
Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide. [GOC:jl, PMID:11746232]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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 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]
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 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]
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 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]
Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity. [GOC:obol]
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]
Modulates the activity of a sodium channel. [GOC:mah]
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]
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 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 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]
The process that gives rise to a glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts. [GOC:mtg_kidney_jan10]
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]
The process in which the developmental fate of a cell becomes restricted such that it will develop into a neuron. [GOC:dph]
Any process that activates or increases the rate or extent of smooth muscle cell proliferation. [CL:0000192, 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 stops, prevents, or reduces the frequency, rate or extent of neuron differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. [GOC:go_curators]
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 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 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 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]
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 cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, 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 process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
The aggregation, arrangement and bonding together of a set of components to form the SKP1-Cullin/Cdc53-F-box protein ubiquitin ligase (SCF) complex. [GOC:pz]
Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs). [GOC:jl, GOC:txnOH, http://www.mblab.gla.ac.uk/, PMID:16858867]
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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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 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]
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 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 zinc (Zn) ions. [GOC:ai]
A multimeric protein complex that acts as an endosomal tethering complex (CORVET = class C core vacuole/endosome tethering) by cooperating with Rab GTPases to capture endosomal vesicles and trap them prior to the action of SNAREs; the complex is involved in endo-lysosomal biogenesis and required for transport between endosome and vacuole. The Saccharomyces cerevisiae complex contains Vps8p, Vps3p, Pep5p, Vps16p, Pep3p, and Vps33p. [PMID:17488625]
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 homotypic fusion of endocytic vesicles to form or add to an early endosome. [PMID:11964142, PMID:9422733]
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 a WW domain of a protein, a small module composed of 40 amino acids and plays a role in mediating protein-protein interactions via proline-rich regions. [PMID:14531730]
Any cytoplasm that is part of a axon. [GO_REF:0000064, GOC:TermGenie, PMID:18667152]
An endosome present in the presynapse that fuses with endocytic vesicles arising in the presynaptic endocytic zone.  This organelle is believed to be involved in regeneration of synaptic vesicles. [PMID:20200227, PMID:25939282]
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 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 heterotetrameric AP-type membrane coat adaptor complex that consists of beta3, delta, mu3 and sigma3 subunits and is found associated with endosomal membranes. AP-3 does not appear to associate with clathrin in all organisms. 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). [GOC:mah, PMID:10611976, PMID:21097499]
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]
The lipid bilayer surrounding an endosome. [GOC:mah]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
The directed movement of neurotransmitter receptor from the postsynaptic endosome in tranpsort vesicles to the lysosome for degradation. [GOC:dos]
A process in which a protein is transported to, or maintained in, a specific location in a membrane. [GOC:mah]
Any process that modulates the rate, frequency, or extent of sequestering of zinc ion. Sequestering of zinc ion is the process of binding or confining zinc ions such that they are separated from other components of a biological system. [GOC:BHF, GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of natural killer T cell differentiation. [ISBN:0781735149, PMID:12154375, PMID:9133426]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the membrane surrounding a synaptic vesicle. [GOC:dph, GOC:jl, GOC:mah, PMID:10620806]
The directed movement of synaptic vesicle along axonal microtubules from the cell body to the presynapse. [GOC:jid, GOC:lmg]
The process in which an antigen-presenting cell expresses lipid antigen of exogenous origin in association with an MHC class Ib protein complex on its cell surface. Class Ib here refers to non-classical class I molecules, such as those of the CD1 family. [GOC:add, PMID:10375559, PMID:15928678, PMID:15928680]
The directed movement of substances from endosomes to the melanosome, a specialised lysosome-related organelle. [PMID:16162817]
A process in which a protein is transported to, or maintained in, a location within an organelle. [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]
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 organelles or molecules along microtubules from the cell body toward the cell periphery in nerve cell axons. [ISBN:0815316194]
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]
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]
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 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]
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]
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 process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure. [GOC:jid]
The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis. [GOC:jid, ISBN:9780878933846]
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 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 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 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]
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 transfer, from NAD, of ADP-ribose to protein amino acids. [GOC:pr, RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295]
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]
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]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor. [EC:2.4.2.30]
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 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 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]
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 is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. [GOC:jl]
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 terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
Any process that stops, prevents or reduces the frequency, rate or extent of ATP biosynthetic process. [GOC:obol]
The process of generating ATP in the nucleus from poly-ADP-D-ribose. Nuclear ATP generation is required for extensive chromatin remodeling events that are energy-consuming. [PMID:27257257]
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]
The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain. [GOC:BHF, GOC:mah, GOC:rl]
The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair. [GOC:ai]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
The process of restoring mitochondrial DNA after damage. [PMID:12565799, PMID:15189144, PMID:16050976]
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). [GOC:bf, GOC:jl]
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]
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 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 chemical reactions and pathways involving mitochondrial DNA. [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]
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 double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix. [GOC:elh]
The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork. [ISBN:071673706X, ISBN:0815316194]
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]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
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 any enzyme. [GOC:jl]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m). [EC:6.5.1.1]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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 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 vesicle that mediates transport between the trans-Golgi network and other parts of the cell. [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 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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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 activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization. [GOC:bf, 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]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Modulates the rate of GTP hydrolysis by a GTPase. [GOC:mah]
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]
Interacting selectively and non-covalently with the frizzled (fz) receptor. [GOC:ceb, PR:000001315]
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 cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm. [GOC:vw, ISBN:0805319409]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
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 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 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 cell motility. [GOC:mah]
The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions. [GOC:add, ISBN:0781735149]
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 modification of histone H3 by the addition of an phosphate group to a threonine residue at position 11 of the histone. [GOC:bf]
Any process that stops, prevents or reduces the rate or extent of B cell proliferation. [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 orderly movement of an epithelial cell from one site to another, often during the development of a multicellular organism. [GOC:ascb_2009, GOC:BHF, GOC:dph, 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]
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 detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell. [GOC:jl, PMID:12142009]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). [GOC:cjm, GOC:mtg_cardio, GOC:mtg_kidney_jan10]
Any process that modulates the frequency, rate, or extent of immunoglobulin production. [GOC:add]
Any process that modulates the frequency, rate, or extent of germinal center formation. [GOC:add]
Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
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]
The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. [GOC:add, ISBN:0781735149, PMID:12956429]
Interacting selectively and non-covalently with an androgen receptor. [GOC:ai]
Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases. [GOC:ebc, PMID:11702775]
Interacting selectively and non-covalently with the enzyme histone deacetylase. [GOC:jl]
Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity. [GOC:jl]
Catalysis of the transfer of a phosphate group to the threonine-11 residue of the N-terminal tail of histone H3. [GOC:bf]
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 the GTP-bound form of the Rho protein. [GOC:mah]
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 protein kinase C. [GOC:jl]
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 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 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 heterodimeric protein complex that possesses an endonuclease activity that specifically cleaves certain types of branched DNA structures; because such structures often form during the replication ribosomal DNA (rDNA) repeats, the complex plays a role in the maintenance of rDNA. The subunits are known as Slx1 and Slx 4 in budding and fission yeasts, and are conserved in eukaryotes. [PMID:14528010, PMID:16467377]
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 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. [ISBN:0198506732]
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 any metal ion. [GOC:ai]
Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis. [PMID:9778254]
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 endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). [EC:3.1.22.4]
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]
Any process that activates or increases the frequency, rate or extent of t-circle formation. [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:22579284]
A telomere maintenance process that results in the formation of a telomeric circle, or t-circle. A t-circle is an extrachromosomal duplex or single-stranded circular DNA molecule composed of t-arrays. T-circles are involved in the control of telomere length via alternative-lengthening of telomeres (ALT) pathway and telomere rapid deletion (TRD). [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:19214183, PMID:19581589, PMID:19809492, PMID:19858100]
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 adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat. [GOC:dph]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
A process in which non-proliferating myoblasts fuse to existing fibers or to myotubes to form new fibers. 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:mtg_muscle]
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 reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. [EC:2.7.10]
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 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]
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 spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules. [GOC:mah, GOC:vw, PMID:11408572, PMID:18367542, PMID:8027178]
A filamentous, cage-like assembly on the nuclear face of the nuclear pore complex (NPC). In S. cerevisiae, Mlp1p and Mlp2p are two major components of the NPC nuclear basket. In vertebrates, Tpr is a major component. [GOC:dgf, PMID:18046406, PMID:19524430, PMID:20947011, PMID:22419078]
An intranuclear focus at which aggregated proteins have been sequestered. [GOC:jl]
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]
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 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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. [ISBN:0198547684]
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]
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 that modulates the frequency, rate or extent of mitotic spindle assembly. [GOC:TermGenie]
Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. [GOC:tb]
Any process that increases the rate, frequency, or extent of the mitotic cell cycle spindle assembly checkpoint, 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:mah, GOC:vw]
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 epidermal growth factor stimulus. [GOC:BHF, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of RNA from the nucleus into the cytoplasm. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus. [GOC:jl]
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-alpha stimulus. Interferon-alpha is a type I interferon. [GOC:sl, PR:000024938]
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]
The directed movement of mRNA from the nucleus to the cytoplasm during a heat stimulus, a temperature stimulus above the optimal temperature for the organism; in particular, a process that enables an organism withstand exposure to temperatures that would otherwise lethally impair poly(A)+ mRNA-nucleus export. [GOC:mah, GOC:vw]
Any process that activates or increases the frequency, rate or extent of heterochromatin formation. [GOC:mah]
Any process that modulates the frequency, rate or extent of mitotic sister chromatid separation. Mitotic sister chromatid separation is the process in which sister chromatids are physically detached from each other during mitosis. [GOC:dph, GOC:tb]
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]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore. [GOC:dph, GOC:jid, GOC:jl, GOC:mah]
The directed movement of molecules between the nucleus and the cytoplasm. [GOC:go_curators]
The directed movement of a protein from the cytoplasm to the nucleus. [GOC:jl]
The directed movement of RNA from the nucleus to the cytoplasm. [GOC:ma]
The import of RNA from the cytoplasm to the nucleus. [GOC:ma]
The directed movement of a MAP kinase to the nucleus upon activation. [PMID:9561267]
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 dynein complex, a protein complex that contains two or three dynein heavy chains and several light chains, and has microtubule motor activity. [GOC:bf, GOC:BHF, GOC:mah]
Interacting selectively and non-covalently with a mitogen-activated protein kinase. [GOC:ai]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
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 monomeric or multimeric forms of tubulin, including microtubules. [GOC:clt]
Enables the directed movement of substances between the nucleus and the cytoplasm of a cell. [GOC:ai]
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]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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]
The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. [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 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 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]
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]
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 large 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]
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]
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 any of the compartments of the Golgi apparatus. [GOC:mah]
The glycosylation of protein via the O3 atom of peptidyl-threonine, forming O3-glycosyl-L-threonine; the most common forms are N-acetylgalactosaminyl, mannosyl, and galactosyl threonine. [RESID:AA0155]
The glycosylation of protein via the O3 atom of peptidyl-serine, forming O3-glycosyl-L-serine; the most common forms are N-acetylgalactosaminyl, mannosyl, galactosyl, and xylosyl serine. [RESID:AA0154]
A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins. [GOC:curators, GOC:pr]
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]
Interacting selectively and non-covalently with manganese (Mn) ions. [GOC:ai]
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]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + polypeptide = UDP + N-acetyl-D-galactosaminyl-polypeptide. This reaction is the modification of serine or threonine residues in polypeptide chains by the transfer of a N-acetylgalactose from UDP-N-acetylgalactose to the hydroxyl group of the amino acid; it is the first step in O-glycan biosynthesis. [EC:2.4.1.41, ISBN:0879695595]
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 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 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]
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 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 feeding behavior. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of cell motility. [GOC:mah]
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 addition of one or more alpha-linked glutamyl units to the gamma carboxyl group of peptidyl-glutamic acid. [RESID:AA0202]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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 complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters. [GOC:krc, GOC:mah, ISBN:0471953393, ISBN:0879695501]
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]
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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum. [GOC:mah]
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. [GOC:curators]
The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I. [GOC:mah, GOC:txnOH]
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 proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage. [GOC:elh, PMID:10197977]
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]
Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA. [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]
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]
Interacting selectively and non-covalently with a heterotrimeric G-protein. [GOC:nln]
Interacting selectively and non-covalently with a complex of G-protein beta/gamma subunits. [GOC:nln, GOC:vw]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Any process that stops or reduces the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
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]
Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins. [GOC:ai]
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]
Conserved heterotrimeric complex of PCNA-like proteins that is loaded onto DNA at sites of DNA damage. [PMID:12531008]
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 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 meiotic cell cycle process that controls cell cycle progression in response to changes in DNA structure by monitoring the integrity of the DNA. The DNA integrity checkpoint begins with detection of DNA damage, defects in DNA structure or DNA replication, and ends with signal transduction. [GOC:mtg_cell_cycle]
A cell cycle checkpoint that acts during a mitotic cell cycle and prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome. [GOC:mtg_cell_cycle]
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 whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. [GOC:go_curators, GOC:isa_complete, 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 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 stops, prevents, or reduces the frequency, rate or extent of DNA replication. [GOC:go_curators]
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]
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]
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]
Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. [GOC:hjd]
The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule. [GOC:elh, PMID:10357855]
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 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]
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 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]
Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-8 secretion. [GOC:obol]
Any process that modulates the frequency, rate or extent of interleukin-8 secretion. [GOC:obol]
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]
The series of events in which a bacterial lipoprotein stimulus is received by a cell and converted into a molecular signal. Bacterial lipoproteins are lipoproteins characterized by the presence of conserved sequence motifs called pathogen-associated molecular patterns (PAMPs). [GOC:jl, PMID:12077222]
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]
Interacting selectively and non-covalently with a component of the extracellular matrix. [GOC:ai]
Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells. [GOC:ecd]
Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids. [GOC:hjd]
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]
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]
A process in which a protein is transported to, or maintained in, a location within a cilium. [GOC:dph]
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]
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 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 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]
Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate. [EC:3.1.3.36, RHEA:22767]
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]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
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 lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat. [GOC:ascb_2009, GOC:dph, GOC:jid, GOC:mah, GOC:tb, ISBN:0716731363, PMID:10219233]
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 process in which a protein is transported to, or maintained in, a location within the endoplasmic reticulum. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the endoplasmic reticulum. [GOC:mah]
The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments. [GOC:mah, PMID:11687502, PMID:14754507]
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]
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]
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 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 stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
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]
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 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 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]
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 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 a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport. [http://www.onelook.com]
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]
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 protein complex that possesses histone acetyltransferase activity. [GOC:mah]
Any process that modulates the frequency, rate or extent of the JAK-STAT signaling pathway. [GOC:bf]
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 RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits. [GOC:txnOH]
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 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 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]
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 the transcription regulatory 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:krc]
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 modulate transcription by RNAP II. [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]
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]
Reactions triggered in response to the presence of a virus that act to protect the cell or organism. [GOC:ai]
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 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]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, 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 a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. [GOC:txnOH]
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 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]
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 viral release from host cell. [GOC:TermGenie, PMID:18305167]
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 activity of a transcription factor, any factor involved in the initiation or regulation of transcription. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the entry of viral entry into a host cell. [GOC:jl]
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]
A process in which a protein is transported to, or maintained at, a microtubule. [GOC:bf, GOC:lb]
Any process that stops, prevents, or reduces the frequency, rate or extent of viral transcription. [GOC:mah]
Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. [GOC:dph, GOC:tb]
Interacting selectively and non-covalently with a phosphorylated protein. [GOC:ai]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
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]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
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 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 nerve cell, e.g. an axon or dendrite. [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]
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]
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 vacuole that functions primarily in the storage of materials, including nutrients, pigments, waste products, and small molecules. [GOC:krc]
Any process that activates or increases the frequency, rate or extent of lamellipodium morphogenesis. [GOC:BHF, GOC:mah]
Any process that modulates the frequency, rate or extent of GTP binding. [GO_REF:0000059, GOC:TermGenie, PMID:19066305, PMID:21454546]
Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading. [GOC:TermGenie, GOC:yaf]
Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell. [GOC:dph]
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]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
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 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 modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of protein binding. [GOC:mah]
Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell. [GOC:mah, ISBN:0815316194]
Any process that increases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium. [GOC:BHF, 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 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]
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]
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]
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]
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 ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B. [GOC:jh, GOC:vw, PMID:10465783, PMID:10611969]
The process in which one or more ubiquitin groups are added to a protein. [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]
A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. [GOC:cilia, GOC:kmv, PMID:21422230]
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 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 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 any TGF-beta receptor signaling pathway. [GOC:mah]
Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized. [GOC:isa_complete]
Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is 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]
Interacting selectively and non-covalently with the beta subunit of the catenin complex. [GOC:bf]
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]
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 involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate 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 a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms. [GOC:ai]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Catalysis of the reaction: citrate = isocitrate. The reaction occurs in two steps: (1) citrate = cis-aconitate + H2O, (2) cis-aconitate + H2O = isocitrate. This reaction is the interconversion of citrate and isocitrate via the labile, enzyme-bound intermediate cis-aconitate. Water is removed from one part of the citrate molecule and added back to a different atom to form isocitrate. [EC:4.2.1.3, GOC:pde, GOC:vw]
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]
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]
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 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 insulin receptor signaling. [GOC:bf]
Any process that activates or increases the frequency, rate or extent of CDK activity. [GOC:go_curators, GOC:pr]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The expansion of a T cell population by cell division. Follows T cell activation. [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]
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. [GOC:go_curators, GOC:mtg_cell_cycle]
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 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 protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
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]
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]
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 or proteins. [GOC:jl]
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 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]
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 monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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]
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 chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome. [GOC:dph, GOC:tb]
The aggregation, arrangement and bonding together of a set of components to form an axonemal dynein inner arm, an inner arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes. [GOC:BHF, GOC:vk, PMID:19944400]
The aggregation, arrangement and bonding together of a set of components to form an axonemal dynein outer arm, an outer arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes. [GOC:BHF, GOC:vk, PMID:19944400]
Any process that modulates the frequency, rate or extent of the activity of an intracellular estrogen receptor signaling pathway. [GOC:mah]
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]
The directed, self-propelled movement of a cilium. [GOC:dph, GOC:jl]
Interacting selectively and non-covalently with an estrogen receptor. [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/]
Interacting selectively and non-covalently with any metal ion. [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 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 modulates the ability of the translational apparatus to interpret the genetic code. [GOC:dph, GOC:tb]
The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-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]
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]
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]
Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. [EC:6, GOC:mah]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: L-isoleucine + ATP + tRNA(Ile) = L-isoleucyl-tRNA(Ile) + AMP + diphosphate + 2 H(+). [EC:6.1.1.5, RHEA:11063]
Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP. [ISBN:0198506732]
The hydrolysis of an incorrectly aminoacylated tRNA. [GOC:hjd, PMID:14663147, PMID:16087889]
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 transfer RNA. [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]
Any process that activates or increases the frequency, rate or extent of stem cell proliferation. [GOC:dph]
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]
The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node. [GOC:mtg_heart]
The commitment of cells to specific cardiac muscle cell fates and their capacity to differentiate into cardiac muscle cells. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. [GOC:mtg_heart]
The developmental process in which the mammary placode forms. The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper. [GOC:dph, PMID:16168142]
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 developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another. [GOC:dph]
The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities. [GOC:dph, ISBN:0721662544]
The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. [GOC:devbiol, GOC:mtg_heart]
The process in which the anatomical structures of the mesoderm are generated and organized. [GOC:go_curators]
The regulated release of follicle-stimulating hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. [ISBN:0198506732]
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 rate or extent of progression through the cell cycle. [GOC:go_curators]
Any process that stops, prevents, or reduces 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 cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
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 frequency, rate or extent of cell proliferation. [GOC:jl]
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]
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, 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 in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping. [UBERON:0002101]
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]
The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. [ISBN:0198506732]
The process whose specific outcome is the progression of the mammary gland 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. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages. [PMID:9576833]
Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation. [GOC:mah]
The process whose specific outcome is the progression of the female genitalia over time, from formation to the mature structure. [GOC:mah]
The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure. [GOC:ems, ISBN:0140512888]
The progression of the limbic system over time from its initial formation until its mature state. The limbic system is a collection of structures in the brain involved in emotion, motivation and emotional aspects of memory. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
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 regionalization process in which information that determines the correct position at which animal organ primordia are formed is generated and perceived resulting in correct positioning of the new animal organ. [GOC:curators]
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]
The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote. [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469). [GOC:PO_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]
The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the atrioventricular bundle. These cells are specialized cardiomyocytes that transmit signals from the AV node to the cardiac Purkinje fibers. [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]
The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:dph, GOC:isa_complete]
The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation. [GOC:dph, PMID:12094232]
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]
The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood. [GOC:hjd, UBERON:0001981]
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/]
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 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 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 an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription. [GOC:txnOH]
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II. [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 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]
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]
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 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 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]
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 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 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 chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate. [GOC:ai]
The directed movement of a cofactor into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A cofactor is a substance that is required for the activity of an enzyme or other protein. [GOC:ai]
Any process that activates, maintains or increases the rate of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes. [GOC:go_curators]
Any process that activates or increases 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, GOC:tb]
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. [CHEBI:33694, GOC:jl]
The chemical reactions and pathways resulting in the breakdown of a protein 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]
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 activity of the enzyme phospholipase A2. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of membrane rafts, small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. [GOC:dph, GOC:jl, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
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 proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Locomotory behavior in a fully developed and mature organism. [GOC:ai]
Learning by associating a stimulus (the cause) with a particular outcome (the effect). [ISBN:0582227089]
The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites. [GOC:jl, GOC:pr]
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 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 process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission. [CHEBI:25512, GOC:dph]
Any process that reduces the pH of the lysosomal lumen, measured by the concentration of the hydrogen ion. [GOC:jid]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases. [GOC:mah]
An endocytosis process that results in the uptake of liquid material by cells from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, called pinosomes, formed by invagination of the plasma membrane. [ISBN:0198506732]
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]
The removal of palymitoyl groups from a lipoprotein. [GOC:hjd]
Catalysis of a hydrolase reaction that removes a palmitoyl moiety from some substrate. [GOC:dos, GOC:pg]
Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate. [EC:3.1.2.2]
Catalysis of the reaction: palmitoyl-protein + H2O = palmitate + protein. [EC:3.1.2.22]
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 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]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
The directed movement of L-ornithine across a membrane. [GO_REF:0000069, GOC:krc, GOC:TermGenie, PMID:8195186]
The directed movement of ornithine, 2,5-diaminopentanoic acid, into, out of or within a mitochondrion. [GOC:ai]
Enables the transfer of L-ornithine from one side of a membrane to the other. L-ornithine is 2,5-diaminopentanoic acid. [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
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 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]
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 a hydrogen peroxide (H2O2) stimulus. [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 an organic substance stimulus. [GOC:sm]
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]
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 plasma membrane surrounding a ruffle. [GOC:mah]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
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]
Any process that activates or increases the frequency, rate or extent of ruffle assembly. [GOC:TermGenie, GOC:yaf]
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]
A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state. [GOC:bf]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rac 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]
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]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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 spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs. [GOC:ab, GOC:krc, GOC:mah, PMID:18322460, PMID:19239890]
A ribonucleoprotein complex that contains small nuclear RNA U5. [GOC:krc, GOC:mah]
The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GOC:krc, 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 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]
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 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]
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]
Any process that modulates the frequency, rate or extent of parathyroid hormone secretion. [GOC:obol]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules by a mechanism that is mediated by DNA, is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. [GOC:mah, GOC:vw]
The adhesion of one platelet to one or more other platelets via adhesion molecules. [GOC:BHF, GOC:vk]
The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud. [GOC:dph, GOC:sdb_2009, GOC:tb]
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. [GOC:dph]
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 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]
The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase. [GOC:dsf, GOC:jid, PMID:16049113]
The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of osteoclast differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of osteoblast differentiation. [GOC:go_curators]
The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue. [GOC:jl, UBERON:0002097]
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 process in which the anatomical structures of the post-embryonic soma are generated and organized. [GOC:ems, ISBN:0140512888]
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, 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 organism over time, from the completion of embryonic development to the mature structure. See embryonic development. [GOC:go_curators]
The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP). [GOC:mah, GOC:signaling]
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 activation of adenylyl cyclase activity and a subsequent increase 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 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 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 chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen. [GOC:mah]
Replacement ossification wherein bone tissue replaces cartilage. [GO_REF:0000034, ISBN:0878932437]
A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function. [GOC:add, GOC:isa_complete]
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/]
Interacting selectively and non-covalently with a complex of G-protein beta/gamma subunits. [GOC:nln, GOC:vw]
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]
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: 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]
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]
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]
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 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 maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome. [GOC:ai, GOC:vw]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
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 process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope. [GOC:dph, GOC:ems, GOC:jl, GOC:mah]
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: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor. [EC:2.4.2.30]
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]
Generation of cells within the nervous system. [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
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 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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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 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]
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 of peptidyl-serine to form peptidyl-O-phospho-L-serine. [RESID:AA0037]
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 modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
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 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]
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 nine-bladed, propeller-like protein complex that links the distal end of the basal body and the cilium to the plasma membrane. Functions in protein sorting and gating (i.e. active and passive transport of proteins in and out of the cilium). [GOC:cilia, GOC:kmv, GOC:krc, PMID:22653444, PMID:24231678, PMID:5064817, PMID:5335827]
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 end of a microtubule that does not preferentially grow (polymerize). [GOC:lb, PMID:23169647]
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 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]
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]
A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome. [GOC:clt, ISBN:0815316194]
The 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates from the centrosome. [GOC:ascb_2009, GOC:dph, GOC:tb]
Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell. [GOC:ai]
Any process in which a microtubule is maintained in a specific location in a cell by attachment to a centrosome. [GOC:BHF, GOC:mah]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules. [GOC:mah, GOC:vw, PMID:11408572, PMID:18367542, PMID:8027178]
A histone acetyltransferase complex that acetylates nucleosomal H3 and H2B and is required for the expression of a subset of Pol II-transcribed genes. The budding yeast complex includes the acetyltransferase Gcn5p, several proteins of the Spt and Ada families, and several TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. [GOC:mah, PMID:10637607, PMID:17337012]
A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues. [PMID:10637607]
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 tubulin deacetylation. Tubulin deacetylation is the removal of an acetyl group from a protein amino acid. [GOC:BHF, GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein. [GOC:bf]
Any process that modulates the frequency, rate or extent of the addition of an acetyl group to a histone protein. [GOC:bf]
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 modulates the frequency, rate or extent of the removal of acetyl groups from histones. [GOC:mah]
The modification of a histone by the addition of an acetyl group. [GOC:ai]
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. [GOC:dph, GOC:ma, GOC:mah, ISBN:0198547684]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
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]
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 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 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]
Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone. [EC:2.3.1.48]
The series of molecular signals generated as a consequence of the insulin receptor binding to insulin. [GOC:ceb]
Interacting selectively and non-covalently with the insulin receptor. [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]
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 extrinsic apoptotic signaling pathway. [GOC:mtg_apoptosis]
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 cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized. [GOC:isa_complete]
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]
Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation. [GOC:BHF, GOC:mah, GOC:rl, PMID:17582821]
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 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]
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]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. [http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
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 process that modulates the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:ai, GOC:hjd]
The large subunit of a ribosome located in the cytosol. [GOC:mtg_sensu]
The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. [GOC:hjd]
Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-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 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]
The smaller subcomplex of the intraciliary transport particle; characterized complexes have molecular weights of 710-760 kDa. [GOC:cilia, GOC:kmv, PMID:14570576]
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 ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
A process in which a protein is transported to, or maintained in, a location within a cilium. [GOC:dph]
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 formation of specific regional progenitor domains along the dorsal-ventral axis in the developing forebrain. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
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]
Any process that modulates the frequency, rate or extent of smoothened signaling. [GOC:go_curators]
A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened. [GOC:mah, PMID:15205520]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
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]
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 formaldehyde (methanal, H2C=O), the simplest aldehyde. [GOC:ai]
Catalysis of the hydrolysis of a carboxylic ester bond. [EC:3.1.1, EC:3.1.1.1, GOC:curators]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Catalysis of the reaction: S-formylglutathione + H(2)O = formate + glutathione + H(+). [EC:3.1.2.12, RHEA:14964]
Catalysis of the hydrolysis of any ester bond. [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]
The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester. [ISBN:0198547684]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Catalysis of the reaction: N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate + H(+) = CO(2) + pantetheine 4'-phosphate. [EC:4.1.1.36, RHEA:16796]
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 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/]
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 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 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 tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group. [ISBN:0198506732]
The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate L-pipecolate. [GOC:mah, MetaCyc:PWY-5283]
Catalysis of the reaction: L-pipecolate + O(2) = 2,3,4,5-tetrahydropyridine-2-carboxylate + H(2)O(2) + H(+). Delta1-piperideine-6-carboxylate is also known as 2,3,4,5-tetrahydropyridine-2-carboxylate. [EC:1.5.3.7, RHEA:11995]
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: H(2)O + O(2) + sarcosine = formaldehyde + glycine + H(2)O(2). [EC:1.5.3.1, RHEA:13316]
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 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 the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds. [MetaCyc:DISULFOXRED-RXN]
A transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIB contains the TATA-binding protein (TBP) and two Pol III-specific proteins, B'' and BRF. [GOC:mah, PMID:11433012]
Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter. [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]
Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, Once recruited to an RNA polymerase III promoter by one or more other transcription factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex. [GOC:txnOH]
The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase III promoter. [GOC:jp, GOC:txnOH, PMID:11387215]
Interacting selectively and non-covalently with an RNA polymerase III transcription factor of the TFIIIC class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III. [GOC:txnOH, PMID:12381659]
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 modulates the frequency, rate or extent of entry of bacterium into host cell. [GOC:obol]
Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. [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 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]
A series of molecular signals initiated by the binding of a chemokine 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 initiates the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical. [GOC:ai]
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]
Any process that activates or increases angiogenesis. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate. [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 fibroblast growth factor stimulus. [GOC:jl, GOC:yaf]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The change in morphology and behavior of a neutrophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor. [GOC:mgi_curators, ISBN:0781735149]
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 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]
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 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]
The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding. [GOC:jl, ISBN:0198506732]
Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. [GOC:mah]
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 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 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]
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]
The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). [ISBN:0198506732]
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 stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin. [GOC:rl, GOC:sm]
Interacting selectively and non-covalently with a chemokine receptor in the CXCR family. [GOC:ceb, PMID:11910892]
The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria. [GOC:BHF, GOC:rl, http://en.wikipedia.org/wiki/Chemokine, http://www.copewithcytokines.de/cope.cgi?key=Cytokines, PMID:12183377]
Interacting selectively and non-covalently with the interleukin-8 receptor. [GOC:go_curators]
Functions to control the survival, growth, differentiation and effector function of tissues and cells. [ISBN:0198599471]
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]
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 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 vesicle fusion. [GOC:mah]
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 Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases. [GOC:mah]
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]
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]
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 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 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]
Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. [GOC:mah, NIF_Subcellular:sao1045389829]
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 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]
The membrane organization process that joins two lipid bilayers to form a single membrane. [GOC:dph, GOC:tb]
Evagination of the presynaptic membrane, resulting in the formation of a new synaptic vesicle. [GOC:curators, PMID:10099709, PMID:20448150]
The process of creating dynamin protein family polymers, compounds composed of a large number of dynamin family monomers around a lipid tube of a dividing mitochondrion. Dynamin polymers form around lipid tubes and contribute to membrane fission. [GOC:ascb_2009, GOC:dph, GOC:tb]
The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments. [PMID:11038192]
Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. [GOC:krc]
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]
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]
Prevention of degradation of telomerase RNA (TERC) molecules. [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:25467444]
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 or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus. [GOC:go_curators]
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]
The process in which a secondary structure of RNA are broken or 'melted'. [PMID:17169986]
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 from a virus. [GOC:hb]
Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. [GOC:mah]
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]
Interacting selectively and non-covalently with the telomerase RNA template. [GOC:krc, PMID:16884717]
Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome. [PMID:16142245, PMID:9512530]
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 the enzyme histone deacetylase. [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 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 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 G-quadruplex RNA structures, in which groups of four guanines adopt a flat, cyclic hydrogen-bonding arrangement known as a guanine tetrad. [PMID:18294969, PMID:18568163, PMID:19330720]
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 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 a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. [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 cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments. [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
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 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 forskolin stimulus. [GO_REF:0000071, GOC:TermGenie, PMID:15937517]
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 follicle-stimulating hormone stimulus. [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]
The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin. [GOC:ceb]
Any process that modulates the rate of GTP hydrolysis by a GTPase. [GOC:jl, GOC:mah]
Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. [GOC:mah]
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 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 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]
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]
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 GPI-anchored ephrin to initiate a change in cell activity. [GOC:mah, PMID:9530499]
Combining with an ephrin to initiate a change in cell activity. [GOC:mah, PMID:9530499]
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]
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]
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 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 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 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]
The dense fibrillar network lying on the inner side of the nuclear membrane. [ISBN:0582227089]
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]
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. [ISBN:0198547684]
The directed movement from the nucleus to the cytoplasm of a tRNA that was previously exported to the cytoplasm and then imported back into the nucleus. The processes of primary tRNA export and secondary export (re-export) can be distinguished because in organisms in which tRNA splicing occurs in the cytoplasm, the export of a mature tRNA must occur by re-export. [GOC:mcc, PMID:17475781, PMID:20032305]
The directed movement of tRNA from the nucleus to the cytoplasm. [GOC:ma]
Enables the transfer of nucleobases, nucleosides, nucleotides and nucleic acids from one side of a membrane to the other. [GOC:ai]
Interacting selectively and non-covalently with transfer RNA. [GOC:ai]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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]
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 the behavior of an organism as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. [GOC:jid]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [GOC:mah]
A protein complex containing myosin heavy chains, plus associated light chains and other proteins, in which the myosin heavy chains are arranged into a filament. [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 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]
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 involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. [GOC:go_curators]
The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated. [GOC:mah, GOC:mtg_muscle, ISBN:0815316194]
A process in which force is generated within skeletal 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. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control. [GOC:mtg_cardio, GOC:mtg_muscle]
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]
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]
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]
Catalysis of movement along a microfilament, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP). [GOC:mah, ISBN:0815316194]
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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
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 the vasculature of the retina is generated and organized. [GOC:BHF, GOC:dph]
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. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes. [GOC:bf, GOC:dph, PMID:11532397, PMID:19619488]
Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription. [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 mediates the transfer of information between the extracellular matrix and a cell. [GOC:bf]
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 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]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Functions to control the survival, growth, differentiation and effector function of tissues and cells. [ISBN:0198599471]
Interacting selectively and non-covalently with the frizzled (fz) receptor. [GOC:ceb, PR:000001315]
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 CMP-N-acetylneuraminate, a substance composed of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid in glycosidic linkage with cytidine monophosphate. [GOC:ai]
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 the reaction: CMP-N-acetylneuraminate + NADPH + H+ + O2 = CMP-N-glycoloylneuraminate + NADP+ + H2O. [EC:1.14.18.2]
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 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 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, to directly drive the active transport of a substance across a membrane. [EC:3.6.1.3, 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]
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]
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 directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:go_curators]
The directed 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. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. [GOC:ai, GOC:krc]
The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:ai, GOC:bf]
Catalysis of the reaction: ATP + H2O + xenobiotic(in) = ADP + phosphate + xenobiotic(out). [EC:3.6.3.44]
Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. [GOC:ai]
A transcriptionally-silent heterochromatin structure present in senescent cells. Contains the condensed chromatin of one chromosome and is enriched for histone modifications. Thought to repress expression of proliferation-promoting genes. [GOC:yaf, PMID:15621527, PMID:21248468]
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 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]
Any process that activates or increases the frequency, rate or extent of cellular senescence. [GOC:BHF]
A cellular senescence process associated with the dismantling of a cell as a response to oncogenic stress, such as the activation of the Ras oncogenic family. [GOC:BHF]
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 assembly of chromatin into senescence-associated heterochromatin foci (SAHF), transcriptionally-silent heterochromatin structures present in senescent cells, containing the condensed chromatin of one chromosome, and enriched for histone modifications. Formation of these chromatin structures is thought to repress expression of proliferation-promoting genes. [GOC:yaf, PMID:15621527, PMID:21248468]
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 from a virus. [GOC:hb]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [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 a retinoid X 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]
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 any enzyme. [GOC:jl]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [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 protein complex that possesses activity that prevents or downregulates transcription. [GOC:mah]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
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 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 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 cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
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 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 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 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]
Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within. [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]
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 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]