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]
A process in which a calcium ion (Ca2+) is transported from one side of a membrane to the other into the mitochondrion by means of some agent such as a transporter or pore. [GOC:vw]
The directed movement of calcium ions (Ca2+) into, out of or within a mitochondrion. [GOC:ai]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
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]
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]
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]
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 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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The directed movement of a lipid hydroperoxide into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:TermGenie]
Any process that activates or increases the frequency, rate or extent of the directed movement of cholesterol within cells. [GOC:mah]
The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:mah, ISBN:0198506732]
The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester. [GOC:ai]
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]
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]
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]
Interacting selectively and non-covalently with oleic acid, the 18-carbon monounsaturated fatty acid (9Z)-octadec-9-enoic acid. [CHEBI:16196, GOC:lp, GOC:mah]
Interacting selectively and non-covalently with a long-chain fatty acyl-CoA. A long-chain fatty acyl-CoA is any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more. [CHEBI:33184, GOC:pm]
Interacting selectively and non-covalently with a sterol, any steroid containing a hydroxy group in the 3 position, closely related to cholestan-3-ol. [CHEBI:15889, GOC:mah]
Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor). [GOC:jl]
Catalysis of the transfer of an 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 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 sterols into, out of or within a cell, or between cells. Sterol are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. [GOC:ai]
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 acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments. [GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
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 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 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 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]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
Any process that modulates the frequency, rate or extent of protein localization to plasma membrane. [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:11602640]
The initial attachment of a transport vesicle membrane to the target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane. Docking requires only that the two membranes come close enough for these proteins to interact and adhere. [GOC:ai, GOC:jid]
The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs. [ISBN:0815316194]
Fusion of the membrane of a transport vesicle with its target membrane. [GOC:jid]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse. [ISBN:0198506732]
Stops, prevents, or reduces the activity of a chloride channel. [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]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The process of 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]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A prolongation or process extending from a cell, e.g. a flagellum or axon. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A 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 blood vessel endothelial cell proliferation involved in sprouting angiogenesis. [GO_REF:0000058, GOC:TermGenie, PMID:23388056]
Any process that stops, prevents or reduces the frequency, rate or extent of peptidyl-serine dephosphorylation. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:11953308]
The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition. [GOC:dph]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
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 modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade. [GOC:ef]
Any process that activates or increases the rate or extent of endothelial cell proliferation. [GOC:add]
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]
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]
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 stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
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 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 any nucleic acid. [GOC:jl]
An endoplasmic reticulum part at which COPII-coated vesicles are produced. [NIF_Subcellular:sao124393998, PMID:15623529, PMID:16957052]
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 formation of a macromolecular complex between the COPII coat proteins and proteins and/or lipoproteins that are going to be transported by the COPII vesicle to the Golgi. [GOC:ascb_2009, GOC:dph, GOC:lb, GOC:tb]
The directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:jl, ISBN:0198506732]
The series of events that restore integrity to a damaged tissue, following an injury. [GOC:bf, PMID:15269788]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. [GOC:go_curators]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion. [GOC:go_curators]
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]
A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This process begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when vesicle fusion is complete. This is the process in which most molecules are secreted from eukaryotic cells. [GOC:mah, ISBN:0716731363]
Any process that activates or increases the frequency, rate, or extent of leukocyte migration. [GOC:add]
Enables the directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells. [GOC:jl, ISBN:0198506732]
The lipid bilayer surrounding any of the compartments of the Golgi apparatus. [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 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 modulates the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus. [GOC:mah]
Any process that increases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of dendrite development. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of phagocytosis. [GOC:ai]
Any process that modulates 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 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]
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 activity of the transcription factor CREB. [GOC:dph, GOC:ecd, GOC:tb]
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 process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
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]
Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states. [GOC:krc]
Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin. [GOC:mah, PMID:11264466]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
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 T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein. [GOC:mah, ISBN:0781735149]
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. [GOC:mah, 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 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]
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. [GOC:dgh, GOC:hb, GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction. [GOC:mgi_curators, PMID:11244041, PMID:11376300]
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of T cell activation. [GOC:ai]
A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell. [GOC:add]
Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine. [GOC:ai]
A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. [GOC:mgi_curators, ISBN:0781735140]
Any process that activates or increases the frequency, rate or extent of alpha-beta T cell proliferation. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2. [GOC:go_curators]
The process of elimination of immature T cells in the thymus which react strongly with self-antigens. [ISBN:0781735149, PMID:12414722]
Any process that activates or increases the rate or extent of T cell proliferation. [GOC:ai]
Any process that activates or increases the frequency, rate, or extent of interleukin-4 production. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. [GOC:add, GOC:mah]
The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation. [ISBN:0781735149]
Any process that 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 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 series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
Any process that activates or increases the frequency, rate, or extent of T cell anergy. [GOC:add]
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
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]
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. [GOC:go_curators, Wikipedia:Transmembrane_receptor]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
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]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Any process that modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, 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]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor. [GOC:dph]
Any process that decreases the rate, frequency or extent of 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 increases the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor. [GOC:dph]
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 activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I. [GOC:go_curators]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. [GOC:dph, GOC:rl, GOC:tb]
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 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 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 an identical protein or proteins. [GOC:jl]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with 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]
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 chemical reactions and pathways resulting in the formation of hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin. [CHEBI:35143, GOC:jl]
The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. [CHEBI:26932, GOC:mah]
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. [GOC:mah]
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. [GOC:curators, ISBN:0198547684]
The chemical reactions and pathways, 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]
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 chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors. [GOC:jl]
The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX. [GOC:go_curators]
The chemical reactions and pathways involving any member of a large group of derivatives or analogs of porphyrin. Porphyrins consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group. [GOC:jl, ISBN:0198506732]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:hjd]
Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. [GOC:mah, ISBN:0198506732]
Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the reaction: glycine + H(+) + succinyl-CoA = 5-aminolevulinate + CO(2) + CoA. [EC:2.3.1.37, RHEA:12924]
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 compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Any process in which a protein is transported to, or maintained at, the juxtaparanode region of an axon. [GOC:BHF, GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The 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 relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. [CL:0000034, GOC:isa_complete]
The process 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 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]
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]
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 a receptor that possesses protein tyrosine kinase activity. [GOC:mah]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
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 lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
The process of removing one or more phosphate groups from a phosphatidylinositol. [ISBN:0198506732]
The process of removing a phosphate group from any mono- or polyphosphorylated inositol. [ISBN:0198506732]
The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol. [CHEBI:28874, ISBN:0198506732]
Catalysis of the 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: 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]
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 coat adaptor complex that links clathrin to a membrane. [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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
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 a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:dph, GOC:TermGenie, PMID:17118486]
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]
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]
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]
Transport of substances into, out of or within a mitochondrion. [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]
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 activates or increases the activity of a GTPase. [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]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [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 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 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 formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres,  and the central core in modular centromeres. [GOC:mah, GOC:vw, PMID:18158900, PMID:19217403]
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 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]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network). [ISBN:0716731363]
The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG. [ISBN:0716731363, PMID:16510524]
Interacting selectively and non-covalently with a class V myosin; myosin V is a dimeric molecule involved in intracellular transport. [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [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 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 modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Any process that modulates the frequency, 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 zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. [GOC:cilia, GOC:clt, PMID:21750193]
The 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]
A protein complex that possesses histone acetyltransferase activity. [GOC:mah]
Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle. [GOC:mtg_cell_cycle]
Any process that decreases the rate, frequency, or extent of the 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 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 H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone. [GOC:jl]
The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 8 of the histone. [GOC:jl]
The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 5 of the histone. [GOC:jl]
The modification of histone H3 by the addition of an acetyl group. [GOC:jl]
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 polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II 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]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. [ISBN:0198547684]
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 terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules. [GOC:elh]
A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. [GOC:dph, GOC:mah]
Any process that activates or increases the frequency, rate or extent of protein localization to nucleolus. [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:24415760]
Any process that activates or increases the frequency, rate or extent of telomeric DNA binding. [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:24415760]
A process in which a protein is transported to, or maintained in, a location within a nucleolus. [GOC:TermGenie, PMID:22809626]
Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome. [GOC:BHF, GOC:mah]
Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of telomeric repeats by telomerase. [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 or extent of the addition of ubiquitin groups to a protein. [GOC:mah]
The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis. [GOC:mah, ISBN:0815316194]
The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase. [GOC:elh]
Interacting selectively and non-covalently with the telomerase RNA template. [GOC:krc, PMID:16884717]
Stops, prevents or reduces the activity of a telomerase. Telomerase catalyzes the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence. [GOC:dph, GOC:krc, GOC:tb]
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 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]
A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus. [GOC:sjw, PMID:9916872]
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 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]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149]
Interacting selectively and non-covalently with any member of the serpin protein family (serine protease inhibitors or classified inhibitor family I4). Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades. The majority of serpins inhibit serine proteases, but serpins that inhibit caspases and papain-like cysteine proteases have also been identified. Rarely, serpins perform a non-inhibitory function; for example, several human serpins function as hormone transporters and certain serpins function as molecular chaperones or tumor suppressors. [GOC:mr, InterPro:IPR000215, PMID:16737556]
Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans. [ISBN:0198506732]
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 hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
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]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
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]
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 interleukin-27 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]
Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism. [GOC:ai]
Any process that modulates the frequency, rate or extent of isotype switching to IgG isotypes. [GOC:jid]
Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. [GOC:add, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response. [GOC:add]
Any process that activates or increases the frequency, rate, or extent of a T-helper 1 type immune response. [GOC:add]
Combining with interleukin-27 and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:jl, GOC:signaling]
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]
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 process in which a potassium ion is transported from one side of a membrane to the other. [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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus. [GOC:mah]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
Development of a cone cell, one of the sensory cells in the eye that reacts to the presence of light. Cone cells contain the photopigment iodopsin or cyanopsin and are responsible for photopic (daylight) vision. [ISBN:0198506732]
Any process in which a protein is transported to, or maintained in, apical regions of the cell. [GOC:bf]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:vw]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate). [GOC:ai]
Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0815340729]
Enables the transmembrane transfer of 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 a cation by a channel that opens when intracellular cAMP has been bound by the channel complex or one of its constituent parts. [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]
Any process that modulates the potential difference across a post-synaptic membrane. [GOC:dph, GOC:ef]
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]
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 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 ubiquitin ligase complex in which a cullin from the Cul2 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein. [PMID:15571813, PMID:15688063]
Any ubiquitin ligase complex in which the catalytic core consists of a member of the cullin family and a RING domain protein; the core is associated with one or more additional proteins that confer substrate specificity. [PMID:15571813, PMID:15688063]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The 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 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 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]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
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]
A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis.  Caveolae may be pinched off to form free vesicles within the cytoplasm. [GOC:mah, ISBN:0721662544, PMID:16645198]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of calcium 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 that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. [GOC:ai]
Any process that modulates the size of blood vessels. [GOC:ai]
Any process that activates or increases angiogenesis. [GOC:go_curators]
The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:jl]
Any process that 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 fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface. [GOC:sl]
A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system. [GOC:mah, GOC:signaling, PMID:15379975]
Any process that activates or increases the frequency, rate or extent of guanylate cyclase activity. [GOC:mah]
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, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2). [CHEBI:18421, GOC:jl]
A process, occurring in smooth muscle, in which there is an increase in cell number by cell division, often leading to an increase in the size of an organ. [GOC:mtg_muscle]
Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle hyperplasia. [GOC:mtg_muscle]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water. [GOC:ai]
The chemical reactions and pathways resulting in the breakdown of arginine, 2-amino-5-(carbamimidamido)pentanoic acid. [CHEBI:29016, GOC:go_curators]
The process in which endothelin modulates the force with which blood passes through the circulatory system. Endothelin is a hormone that is released by the endothelium, and it is a vasoconstrictor. [GOC:mtg_cardio]
The regulation of the force of heart muscle contraction mediated by chemical signaling, hormonal, autocrine or paracrine. [GOC:mtg_cardio, GOC:rl]
Any process that modulates 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]
The reorganization or renovation of existing blood vessels. [GOC:hjd]
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 leading to the rupture of the follicle, releasing the centrally located oocyte into the oviduct. An example of this is found in Mus musculus. [GOC:mtg_sensu, http://ovary.stanford.edu]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes. [GOC:BHF, GOC:sjp, PMID:10433269, Wikipedia:Scaffold_protein]
Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. [GOC:ai]
Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid. [CHEBI:29016, GOC:BHF, GOC:rl]
Interacting selectively and non-covalently with a tetrahydrobiopterin, 5,6,7,8-tetrahydrobiopterin or a derivative thereof; tetrahydrobiopterins are enzyme cofactors that carry electrons in redox reactions. [CHEBI:15372, GOC:BHF, GOC:mah, GOC:rl]
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, 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 flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. [GOC:tb]
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 iron (Fe) ions. [GOC:ai]
Catalysis of the reaction: L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+. [EC:1.14.13.39]
Interacting selectively and non-covalently with monomeric actin, also known as G-actin. [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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
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 any nucleic acid. [GOC:jl]
A protein complex that consists of members of the Bcl-2 family of anti- and proapoptotic regulators. Bcl-2 proteins respond to cues from various forms of intracellular stress, such as DNA damage or cytokine deprivation, and interact with opposing family members to determine whether or not the caspase proteolytic cascade should be unleashed. [GOC:so, PMID:14634621]
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 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]
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 extrinsic apoptotic signaling pathway in absence of ligand. [GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of response to DNA damage stimulus. [GOC:obol]
Any process that stops, prevents or reduces the frequency, rate or extent of anoikis. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of oxidative stress-induced neuron intrinsic apoptotic signaling pathway. [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis, PMID:15044679, PMID:20816705]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that modulates the occurrence or rate of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus. [GOC:sl]
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]
The morphological and physiological alterations undergone by mitochondria during apoptosis. [GOC:mah, GOC:mtg_apoptosis]
A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered. [GOC:go_curators, GOC:mtg_apoptosis]
Interacting selectively and non-covalently with the BH3 domain of a protein of the Bcl-2 family. The BH3 domain is a potent death domain and has an important role in protein-protein interactions and in cell death. [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01259]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [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]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Interacting selectively and non-covalently with an 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]
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 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 process of removing one or more phosphoric residues from a protein. [GOC:hb]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
A nuclear body associated with the histone gene locus that is thought to contain all of the factors necessary for histone mRNA transcription and pre-mRNA processing. In Drosophila, U7 snRNP is located in the histone locus body rather than the distinct Cajal body. [GOC:sart, PMID:16533947, PMID:18927579, PMID:19620235]
The ordered and organized complex of DNA and protein that forms regions of the chromosome that are being actively transcribed. [GOC:sart, PMID:17965872]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
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]
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]
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 III promoter. [GOC:go_curators, GOC:txnOH]
The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter. [GOC:jl, ISBN:0321000382]
The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter. [GOC:jl, ISBN:0321000382]
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 modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits. [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 translational elongation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The removal of the ubiquitin group from a monoubiquitinated histone H2A protein. [GOC:bf, PMID:18226187, PMID:20436459]
The removal of one or more ubiquitin groups from a protein. [GOC:ai]
The modification of histones by removal of ubiquitin groups. [GOC:ai]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
A 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 results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein. [GOC:go_curators]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, 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 any metal ion. [GOC:ai]
Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation. [GOC:ecd]
Interacting selectively and non-covalently with 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 thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin. [EC:3.4.19.12, GOC:bf, GOC:ka]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein. [GOC:jh2, ISBN:0120793709]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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]
Interacting selectively and non-covalently with a lipid. [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]
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]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
The 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 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 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 inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The cleavage of peptide bonds in proteins, usually near the N terminus, contributing to the process of import into the mitochondrion. Several different peptidases mediate cleavage of proteins destined for different mitochondrial compartments. [GOC:mcc, PMID:12191769]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
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 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 multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar. [GOC:go_curators, ISBN:0198506732]
The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate. [GOC:ai]
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. [GOC:ai]
Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate. [GOC:jl]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. [EC:2.7.4.6]
Catalysis of the reaction: ATP + (d)CMP = ADP + (d)CDP. [EC:2.7.4.14]
Catalysis of the reaction: ATP + AMP = 2 ADP. [EC:2.7.4.3]
Any cytoplasm that is part of a axon. [GO_REF:0000064, GOC:TermGenie, PMID:18667152]
Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity. [GOC:BHF, 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]
Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. [GOC:go_curators, 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]
Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. [GOC:mtg_muscle, 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]
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]
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 apoptotic signaling pathway. [GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of endothelial cell chemotaxis. [GOC:BHF]
Any process that stops, prevents or reduces the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway. [GOC:BHF, GOC:mtg_apoptosis, GOC:TermGenie, PMID:11672522]
The directed movement of proteins along microtubules from the cell body toward the cell periphery in nerve cell axons. [GOC:dos]
The adhesion of one platelet to one or more other platelets via adhesion molecules. [GOC:BHF, GOC:vk]
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 activates or increases angiogenesis. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels. [GOC:go_curators]
Any process that modulates I-kappaB kinase/NF-kappaB signaling. [GOC:jl, PMID:12773372]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. [GOC:jl, PMID:10891884]
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]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production. [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 virus. [GOC:hb]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. [GOC:hjd]
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 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 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]
Stops, prevents or reduces the activity of protein kinase C, an enzyme which phosphorylates a protein. [GOC:ai]
Interacting selectively and non-covalently with protein kinase C. [GOC:jl]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
The chemical reactions and pathways resulting in the formation of acetyl-CoA from acetate, either directly or via acetylphosphate. [MetaCyc:ACETATEUTIL-PWY]
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 AMP, adenosine monophosphate. [GOC:go_curators]
Catalysis of the reaction: ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA. [EC:6.2.1.1]
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]
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. [GOC:go_curators]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [GOC:go_curators]
The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated. [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 addition of an adenylyl group (adenosine 5'-monophosphate; AMP) to a protein amino acid. [GOC:ai, GOC:jsg, GOC:sart, PMID:21607083]
Catalysis of the reaction: ATP + protein = diphosphate + adenylyl-protein; mediates the addition of an adenylyl (adenosine 5'-monophosphate; AMP group) to specific residues of target proteins. [GOC:mah, PMID:19039103, PMID:19362538]
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 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]
An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size. [PMID:14732047]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus. [GOC:sl]
Any process that 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 phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine. [RESID:AA0037]
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 introducing a phosphate group on to a protein. [GOC:hb]
Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
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 reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions are dependent on the presence of calcium ions. [GOC:mah]
Interacting selectively and non-covalently with 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]
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 reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin. [GOC:mah, PMID:11264466]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. [GOC:bf]
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 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 structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a 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:jl]
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 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 reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate. [EC:3.1.3.48]
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 an rRNA molecule. [GOC:mah]
The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically. [GOC:curators]
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 dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor. [ISBN:1555811337, PMID:10690410]
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 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 nucleic acid. [GOC:jl]
A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein. [PMID:16792691, PMID:18223036, PMID:18552200]
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 ubiquitin ligase complex in which a cullin from the Cul4B subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by unknown subunits. [PMID:15571813, PMID:15688063]
A ubiquitin ligase complex in which a cullin from the Cul4A subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein. [PMID:15571813, PMID:15688063]
Any ubiquitin ligase complex in which the catalytic core consists of a member of the cullin family and a RING domain protein; the core is associated with one or more additional proteins that confer substrate specificity. [PMID:15571813, PMID:15688063]
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]
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 terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
Any process that activates or increases the frequency, rate or extent of viral release from host cell. [GOC:TermGenie, PMID:18305167]
Any process that modulates the frequency, rate or extent of mitotic cell cycle phase transition. [GOC:mtg_cell_cycle, GOC:TermGenie, PMID:22841721]
A DNA repair process that is initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced damage site. UV-damage excision repair acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs). [GOC:mah, PMID:9619100]
An interaction between two organisms living together in more or less intimate association. The term symbiont is used for the smaller (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. [GOC:cc]
Any process where the infecting virus increases the levels of viral proteins in a cell. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of viral genome replication. [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 ubiquitin, and mediated by the proteasome. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The 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 modification of histone H2A by addition of a single ubiquitin group. [PMID:18206970]
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]
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 damaged DNA. [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 the parathyroid gland over time, from its formation to the mature structure. The parathyroid gland is an organ specialised for secretion of parathyroid hormone. [GOC:dph, ISBN:0721662544]
The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. [DOI:10.1371/journal.pone.0051070, GOC:cjm, http://www.onelook.com]
The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113]
The process 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 pertaining to the initial formation of an animal organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ. [GOC:dph, GOC:jid]
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 the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone. [GOC:dgh]
The process in which the anatomical structure of the glossopharyngeal nerve is generated and organized. Various sensory and motor branches of the glossopharyngeal nerve supply nerve connections to the pharynx and back of the tongue. The branchial motor component contains motor fibers that innervate muscles that elevate the pharynx and larynx, and the tympanic branch supplies parasympathetic fibers to the otic ganglion. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
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]
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]
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. [GOC:dgh, GOC:go_curators, ISBN:0471245208, ISBN:0721662544]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The 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]
The reorganization or renovation of existing blood vessels. [GOC:hjd]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
Interacting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. [GOC:yaf, InterPro:IPR009071, PMID:18445004]
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]
The portion of the plasma membrane surrounding the brush border. [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]
The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. [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 amino acids, organic acids containing one or more amino substituents across a membrane by means of some agent such as a transporter or pore. [GOC:dph, GOC:tb]
Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. [GOC:mtg_transport, ISBN:0815340729, PMID:10839820]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: neurotransmitter(out) + Na+(out) = neurotransmitter(in) + Na+(in). [TC:2.A.22.-.-]
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 protein targeting to mitochondrion. [GO_REF:0000058, GOC:pad, GOC:PARL, GOC:TermGenie, PMID:24270810]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with a G-protein coupled receptor. [GOC:ceb, GOC:dph]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of 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 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 any nucleic acid. [GOC:jl]
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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A proton-transporting ATP synthase complex found in the mitochondrial membrane. [GOC:mah, GOC:mtg_sensu]
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 mitophagy in response to mitochondrial depolarization. [GO_REF:0000058, GOC:pad, GOC:PARL, GOC:TermGenie, PMID:22020285]
Any process that modulates the frequency, rate or extent of ATP metabolic process. [GO_REF:0000058, GOC:TermGenie, PMID:20695849]
Any process that modulates the frequency, rate or extent of protein targeting to mitochondrion. [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
Any process that activates or increases the frequency, rate or extent of proteolysis involved in cellular protein catabolic process. [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:18307834]
Any process that activates or increases the frequency, rate or extent of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway. [GOC:BHF, GOC:mtg_apoptosis, GOC:TermGenie]
The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers. [CHEBI:26523, GOC:mah]
The process in which the potential difference across the mitochondrial membrane is reduced from its steady state level. [Wikipedia:Depolarization, Wikipedia:Mitochondrion]
Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. [GOC:ai]
Any process that stops or reduces the rate of ATP hydrolysis by an ATPase. [GOC:mah]
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. [GOC:mah]
The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors. [GOC:jl]
Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation. [GOC:add]
Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP. [GOC:ai]
Interacting selectively and non-covalently with angiostatin, a proteolytic product of plasminogen or plasmin containing at least one intact kringle domain, and which is an inhibitor of angiogenesis. [PMID:16043488]
Stops, prevents or reduces the activity of any enzyme that catalyzes the hydrolysis of ATP to ADP and orthophosphate. [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 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]
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 chloride across a membrane. [GOC:TermGenie, GOC:vw]
The controlled release of arachidonic acid from a cell or a tissue. [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 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, PMID:10203867, PMID:12723742, PMID:12843304, Wikipedia:Pain]
Any intracellular signal transduction in which the signal is passed on within the cell via an inositol phosphate. Includes production of the inositol phosphate, and downstream effectors that further transmit the signal within the cell. Inositol phosphates are a group of mono- to poly-phosphorylated inositols, and include inositol monophosphate (IP), inositol trisphosphate (IP3), inositol pentakisphosphate (IP5) and inositol hexaphosphate (IP6). [GOC:bf, GOC:ceb, GOC:signaling, ISBN:0198506732, PMID:11331907]
A series of molecular signals that leads to the upregulation of calcium-dependent phospholipase A2 activity in response to the signal. [GOC:dph, GOC:jl, GOC:tb]
The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites. [GOC:jl, GOC:pr]
The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. [GOC:bf, GOC:jid, ISBN:0582227089]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
Any process that increases the concentration of calcium ions in the cytosol. [GOC:ai]
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]
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 calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
An eating behavior process whereby detection of a dietary excess results in a decrease in intake of nutrients. [GOC:pg, GOC:pr, PMID:12161655, PMID:12840200]
Interacting selectively and non-covalently and stoichiometrically with neuromedin U, a hypothalamic peptide involved in energy homeostasis and stress responses. [GOC:jl, PMID:12584108]
Combining with a neuropeptide to initiate a change in cell activity. [GOC:ai]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Enables the transmembrane transfer of chloride by a channel that opens in response to stimulus by a calcium ion or ions. Transport by a channel involves catalysis of facilitated diffusion of a solute (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel, without evidence for a carrier-mediated mechanism. [GOC:mtg_transport]
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 neuromedin U to initiate a change in cell activity. [GOC:ai]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A tubular array of microtubules that extends from the perinuclear ring surrounding the spermatid nucleus to the flagellar axoneme. The manchette may also contain F-actin filaments. [GOC:krc, PMID:15018141, PMID:22319670, PMID:24440897, PMID:26792866]
The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. [GOC:jl]
Interacting selectively and non-covalently with the microtubule constituent protein alpha-tubulin. [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]
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A protein complex 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 lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell. [GOC:ai]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [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 membrane organization process that joins two lipid bilayers to form a single membrane. [GOC:dph, GOC:tb]
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. [GOC:mah]
Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse. [ISBN:0198506732]
Interacting selectively and non-covalently with both N-ethylmaleimide-sensitive fusion protein (NSF) and a cis-SNARE complex (i.e. a SNARE complex in which all proteins are associated with the same membrane) and increasing the ATPase activity of NSF, thereby allowing ATP hydrolysis by NSF to disassemble the cis-SNARE complex. [GOC:mah, PMID:14570579, PMID:15556857]
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 in which mRNA is transported to, or maintained in, a specific location within the 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]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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 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 stops, prevents or reduces the frequency, rate or extent of telomere maintenance via telomere lengthening. [GO_REF:0000058, GOC:BHF, GOC:nc, GOC:TermGenie, PMID:23959892]
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 increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. [GOC:tb]
The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein. [GOC:BHF, GOC:rl]
Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome. [GOC:BHF, GOC:mah]
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]
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 transfer, from NAD, of ADP-ribose to protein amino acids. [GOC:pr, RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Interacting selectively and non-covalently with any enzyme. [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 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]
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]
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]
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 aggregation, arrangement and bonding together of a set of components to form a clathrin-coated pit. [GO_REF:0000079, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353]
The directed movement of substances from the Golgi to lysosomes. [GOC:ascb_2009, GOC:dph, GOC:tb]
The directed movement of a protein to a specific location in the plasma membrane. [GOC:dph, GOC:tb]
The directed movement of a protein to a specific location in the Golgi apparatus. [GOC:mah]
An endocytosis process that begins when material is taken up into clathrin-coated pits, which then pinch off to form clathrin-coated endocytic vesicles. [GOC:BHF, GOC:mah, PMID:18498251, PMID:8970738, PMID:9234965]
The disaggregation of a clathrin coat into its constituent components; results in stripping or removing the clathrin coat from clathrin-coated vesicles (CCV) before fusing with their targets. CVVs transport cargo from plasma membrane and trans-Golgi to the endosomal system. [PMID:11084334, PMID:11146663, PMID:8524399]
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]
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]
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 process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The pronucleus originating from the spermatozoa that was involved in fertilization. [GOC:hjd, ISBN:0198506732]
The pronucleus originating from the ovum that is being fertilized. [GOC:hjd, ISBN:0198506732]
The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone. [GOC:BHF, GOC:se, GOC:tb]
The removal of a methyl group from one or more nucleotides within an DNA molecule. [PMID:17208187]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The active DNA demethylation of the paternal genome that takes place before the first cell division. [GOC:sp, PMID:22868271]
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]
Catalysis of the reaction: methylcytosine + 2-oxoglutarate + O2 = 5-hydroxymethylcytosine + succinate + CO2. [PMID:19372391]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
The lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The lipid bilayer surrounding any of the compartments of the Golgi apparatus. [GOC:mah]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
The 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]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient. [GOC:ecd, GOC:mah, ISBN:0198547684]
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 protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone. [GOC:mtg_sensu, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
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 results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl, PMID:12115731]
Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. [ISBN:0198506732]
Catalysis of the reaction: NADH + H+ + ubiquinone = NAD+ + ubiquinol. [EC:1.6.5.3]
Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA. [GOC:editors, GOC:mah, ISBN:0198547684, PMID:19239890]
The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced. [GOC:krc, ISBN:0198506732, ISBN:0879695897]
The portion of the cytoskeleton that lies just beneath the plasma membrane. [GOC:mah]
The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. [ISBN:0815316194]
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 lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome. [PMID:11019806, PMID:12186635, PMID:14570571]
A 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 process whose specific outcome is the progression of a lens fiber cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a lens fiber cell fate. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye. [GOC:mah, PMID:7693735]
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]
Formation of myofibrils, the repeating units of striated muscle. [GOC:mah]
Locomotory behavior in a fully developed and mature organism. [GOC:ai]
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]
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]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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 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]
The chemical reactions and pathways involving any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals. Vitamin K substances share a methylated naphthoquinone ring structure and vary in the aliphatic side chains attached to the molecule. [GOC:jl, http://www.dentistry.leeds.ac.uk/biochem/thcme/vitamins.html#k]
Catalysis of the reaction: 2-methyl-3-phytyl-1,4-naphthoquinone + oxidized dithiothreitol + H2O = 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl-1,4-naphthoquinone + 1,4-dithiothreitol. [EC:1.1.4.1, MetaCyc:1.1.4.1-RXN]
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 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]
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]
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 lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
Any process that increases the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of triglyceride. [GOC:rn, GOC:tb]
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. [ISBN:0198547684]
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 hydrolysis of a carboxylic ester bond. [EC:3.1.1, EC:3.1.1.1, GOC:curators]
Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. [GOC:jl]
Catalysis of the hydrolysis of a substrate by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [Wikipedia:Serine_hydrolase]
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: triacylglycerol + H2O = diacylglycerol + a carboxylate. [EC:3.1.1.3]
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]
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 frequency, rate or extent of peptidase activity, the hydrolysis 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]
Binds to and increases the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds. [GOC:ai]
Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with 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 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 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 carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide. [GOC:dos, GOC:vw]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2). [GOC:jl]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. [GOC:mah]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. [GOC:jl, PMID:12115731]
Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [CHEBI:30413, GOC:ai]
The action of a molecule that contributes to the structural integrity of the extracellular matrix. [GOC:mah]
Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O. [EC:1.11.1.7]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. [GOC:mah]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group. [EC:2.7.7.7, GOC:vw, ISBN:0198547684]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
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 which usually consists of three components, e.g. in Xenopus, the importin alpha and beta-subunits and any protein which has a nuclear localization sequence (NLS). The complex acts to import proteins with an NLS into the nucleus through a nuclear pore. [GOC:jl, PMID:9323123, PMID:9323134]
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 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 activates or increases the frequency, rate or extent of anoikis. [GOC:mah]
A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered. [GOC:mah, GOC:mtg_apoptosis]
Any process that increases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of glucose. [GOC:jl]
Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours. [GOC:mah]
A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. [GOC:mtg_electron_transport, ISBN:0716720094]
The directed movement of molecules between the nucleus and the cytoplasm. [GOC:go_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]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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 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]
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]
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 type of extracellular matrix found in interstitial connective tissue, characterized by the presence of fibronectins, proteoglycans, and types I, III, V, VI, VII and XII collagens. [PMID:8450001]
A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus. [GOC:mtg_sensu, ISBN:0198547684]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. [GOC:mah]
Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules. [GOC:dph, GOC:pf, GOC:tb]
Interacting selectively and non-covalently with a type V collagen trimer. [GOC:BHF, GOC:mah]
Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with 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 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]
Interacting selectively and non-covalently with the DNA portion of a nucleosome. [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]
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 ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. [GOC:elh, PMID:20404130]
Any process that modulates the frequency, rate or extent of stem cell differentiation. [GOC:obol]
Any process that modulates the frequency, rate or extent of stem cell population maintenance. [GOC:obol]
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]
The chemical reactions and pathways resulting in the formation of formaldehyde (methanal, H2C=O), the simplest aldehyde. [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 modification of histone H3 by addition of two methyl groups to lysine at position 9 of the histone. [GOC:vw]
The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone. [GOC:mah]
Any series of molecular signals generated as a consequence of an androgen binding to its receptor. [GOC:mah]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
A series of molecular signals mediated by the detection of a hormone. [GOC:sm]
The change in shape of the spermatid nucleus from a spherical structure to an elongated organelle, during the latter part of spermatid differentiation. [GOC:bf, GOC:dph, GOC:jl, GOC:mah, ISBN:0879694238]
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]
Interacting selectively and non-covalently with an androgen receptor. [GOC:ai]
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein. [PMID:16362057]
Interacting selectively and non-covalently with DNA that is assembled into chromatin. [GOC:mah]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH]
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]
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]
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 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 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 granulocyte macrophage colony-stimulating factor receptor. [GOC:ai]
Functions to control the survival, growth, differentiation and effector function of tissues and cells. [ISBN:0198599471]
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 process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand. [GOC:mtg_apoptosis]
The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. [CL:0000451, GOC:pr]
Any process that activates or increases the rate or extent of podosome assembly. [GOC:mah, GOC:sl]
Any process that stops, prevents, or reduces the frequency, rate or extent of cytolysis. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of DNA replication. [GOC:go_curators]
The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. [CL:0000782, GOC:jl]
Any process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat5 protein. [GOC:jl, PMID:11426647]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
Any process that activates or increases the frequency, rate, or extent of interleukin-23 production. [GOC:mah]
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. [GOC:mah]
The process in which a myeloid precursor cell acquires the specialized features of a neutrophil. [GOC:mah]
Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions. [GOC:add, GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin. [GOC:add, ISBN:068340007X]
The 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 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]
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]
Transcription factor complex consisting of ATF4 and CREB1 subunits that is capable of binding to cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3') as part of the positive regulation of transcription. Regulatory targets include the GRP78 (HSPA5) promoter in humans, whose activation by this complex is part of the ER stress response pathway. [GOC:bhm, IntAct:EBI-10043081, IntAct:EBI-10043332, PMID:12871976]
The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin. [ISBN:0198506732]
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]
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 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 zinc ion stimulus. [GOC:mah]
The process in which a relatively unspecialized cell acquires specialized features of a Type I pneumocyte. A type I pneumocyte is a flattened cell with greatly attenuated cytoplasm and a paucity of organelles. [GOC:dph, GOC:mtg_lung, ISBN:0721662544]
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 biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung. [GOC:dph, GOC:mtg_lung]
Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle tissue development. [GOC:vk]
Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell. [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 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 adipocyte differentiation. [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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size. [GOC:dph, GOC:go_curators, GOC:tb]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus. [GOC:bf]
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 glucagon stimulus. [GOC:sl]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. [GOC:mah]
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]
The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands. [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 DNA-dependent transcription using a mechanism that involves direct competition for interaction with a promoter binding site. [GOC:tb]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. [GOC:sm]
Any process that modulates the size of a cell. [GOC:go_curators]
Any biological process in an organism that recurs with a regularity of approximately 24 hours. [GOC:bf, GOC:go_curators]
The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task). [GOC:curators, http://www.onelook.com/, ISBN:0582227089]
The secretion of milk by the mammary gland. [ISBN:0198506732]
De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon. [GOC:dph, GOC:jid, GOC:pg, GOC:pr, ISBN:0198506732]
The process of introducing a phosphate group on to a protein. [GOC:hb]
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 an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with the cyclic AMP response element (CRE), a short palindrome-containing sequence found in the promoters of genes whose expression is regulated in response to cyclic AMP. [PMID:2875459, PMID:2900470]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. [GOC:txnOH]
Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription. [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 basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [GOC:go_curators]
Any process that 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 glucose stimulus. [GOC:mah]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. [GOC:BHF, 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]
Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. [GOC:ai]
The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile. [GOC:go_curators]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [CHEBI:30413, GOC:ai]
Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. [GOC:mah]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: cholesterol + NADPH + H+ + O2 = 7-alpha-hydroxycholesterol + NADP+ + H2O. [EC:1.14.13.17]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water. [http://www.onelook.com/, ISBN:0198506732]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
The 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 membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The 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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that modulates the frequency, rate or extent of N-methyl-D-aspartate selective glutamate receptor activity. [GOC:BHF]
Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors. [GOC:TermGenie, PMID:17245429]
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. [GOC:mtg_apoptosis]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH. [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 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 activity of a cysteine-type endopeptidase 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]
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 chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
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]
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 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 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 process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with the SNAP receptor syntaxin-1. [GOC:ai]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states. [GOC:krc]
Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin. [GOC:mah, PMID:11264466]
Catalysis of the 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 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 ceramides, any N-acylated sphingoid. [ISBN:0198547684]
Catalysis of the reaction: H(2)O + sphingomyelin = ceramide + choline phosphate + H(+). [EC:3.1.4.12, RHEA:19256]
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 part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization. [GOC:mah]
Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell. [GOC:dph, GOC:tb]
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]
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]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N(omega)-dimethyl-L-arginine. [RESID:AA0068, RESID:AA0069]
The modification of histones by addition of methyl groups. [GOC:ai]
The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. [GOC:ai]
The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. [GOC:go_curators, GOC:mtg_sensu]
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 addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues. [EC:2.1.1.319, PMID:14705965, RESID:AA0068, RESID:AA0069]
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: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine. [GOC:mah, PMID:12351636]
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]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Any process that stops, prevents, or reduces the frequency, rate or extent of 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 the enzyme histone acetyltransferase. [GOC:bf]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to 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 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 morphogenesis process in which the ductus arteriosus changes to no longer permit blood flow after birth. The ductus arteriosus is the shunt between the aorta and the pulmonary artery which allows blood to bypass the fetus' lungs. [GOC:hw]
The process in which the population of cells that make up a mesenchyme undergo directed movement. [GOC:ascb_2009, GOC:dph, GOC:tb]
The process whose specific outcome is the progression of the ureter over time, from its formation to the mature structure. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut. [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]
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 a cytokine stimulus. [GOC:mah]
The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland alveolus. [GOC:dph, GOC:yaf]
The progression of the venous blood vessel over time from its initial formation to the mature structure. Venous blood vessels carry blood back to the heart after the capillary bed. [GOC:dph, GOC:sdb_2009, GOC:tb]
The process in which the anatomical structures of a lung lobe are generated and organized. A lung lobe is a projection that extends from the lung. [GOC:dph]
The process in which anatomical structures of the right lung are generated and organized. [GOC:dph, GOC:mtg_lung]
The process in which the anatomical structures of branches in the open tracheal system are generated and organized. [GOC:dph]
The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. [GOC:dph, GOC:mtg_lung]
The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches. [GOC:dph]
The biological process whose specific outcome is the progression of a lung vasculature from an initial condition to its mature state. This process begins with the formation of the lung vasculature and ends with the mature structure. The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs. [GOC:dph, GOC:mtg_lung]
The process in which the anatomical structures of the lung are generated and organized. [GOC:dph]
Any process that modulates the frequency, rate or extent of smooth muscle cell differentiation. [CL:0000192, GOC:ai]
The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary. [CL:0000192, GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. [GOC:ai]
The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase. [GOC:jid, GOC:rc]
The process, occurring during the embryonic phase, by which the anatomical structures of the ectodermal digestive tract are generated and organized. [GOC:jid, GOC:rc]
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 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]
The process in which the anatomical structures of the digestive tract are generated and organized during embryonic development. The digestive tract is the anatomical structure through which food passes and is processed. [GOC:go_curators]
The process in which a relatively unspecialized cell acquires the specialized features of a lateral mesoderm cell. [GOC:jid]
The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways. [GOC:mtg_lung, PMID:9751757]
Any process that activates or 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 specification and formation of the apicobasal polarity of an epithelial cell. [GOC:ascb_2009, GOC:bf, GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces the rate of mast cell degranulation. [ISBN:0781735149]
The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes. [GOC:cvs]
Any process that activates or increases the frequency, rate or extent of cell migration. [GOC:go_curators]
The process whose specific outcome is the progression of the 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 whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract. [GOC:jid]
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 attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism. [GOC:hb]
The series of events by which an injury stimulus is received and converted into a molecular signal. [GOC:mtg_muscle]
Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules. [GOC:dph, GOC:pf, GOC:tb]
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 process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:jid, UBERON:0000948]
The process whose specific outcome is the progression of the 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 midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine. [GOC:jid, UBERON:0001045]
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 generated as a consequence of activation of the transmembrane protein Smoothened. [GOC:mah, PMID:15205520]
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 process in which the left cardiac ventricle is generated and organized. [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 of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells. [GOC:dph]
The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes. [ISBN:0721662544]
The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. [ISBN:0721662544]
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 differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes. [PMID:8999798]
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]
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 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 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 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 synapse that uses GABA as a neurotransmitter.  These synapses are typically inhibitory. [GOC:dos]
A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
A protein complex that forms a transmembrane channel through which chloride ions may pass in response to glycine binding to the channel complex or one of its constituent parts. [GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
The directed movement of chloride across a membrane. [GOC:TermGenie, GOC:vw]
The receptor clustering process in which gamma-aminobutyric acid (GABA) receptors are localized to distinct domains in the cell membrane. [GOC:BHF, GOC:sjp, PMID:15620359]
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]
A reflex process in which an animal immediately tries to turn over after being placed in a supine position. [GOC:dph, PMID:8635460]
The process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. [GOC:dph]
Any process pertaining to the functions of the nervous and muscular systems of an organism. [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 amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. [CHEBI:33709, GOC:ef, GOC:mlg]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg. [GOC:jid, GOC:pr, ISBN:0198606907]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
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]
The vesicular release of classical neurotransmitter molecules from a neuron, across a chemical synapse, the subsequent activation of neurotransmitter receptors of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. [GOC:jl, MeSH:D009435]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
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]
An action or movement due to the application of a sudden unexpected stimulus. [GOC:dph]
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]
Enables the transmembrane transfer of an 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]
Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease. [GOC:jl, ISBN:0198506732]
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 protein complex that binds to heme and to pri-miRNAs, and is required for the formation of a pre-microRNA (pre-miRNA), the initial step of microRNA (miRNA) biogenesis. The complex is composed of the double-stranded-RNA-specific RNase Drosha (also called RNASEN) and the RNA-binding protein DGCR8 (heme-free or heme-bound forms). Within the complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs RNASEN/Drosha to cleave the 3' and 5' strands of a stem-loop to release hairpin-shaped pre-miRNAs. [PMID:16963499, PMID:17159994]
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 involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. [GOC:dph, GOC:tb]
The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis. [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]
Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule. [GOC:sl, PMID:15211354]
Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding. [GOC:sl, PMID:15531877, PMID:15574589]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [CHEBI:30413, GOC:ai]
Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt. [PMID:11157775, PMID:15242644]
Interacting selectively and non-covalently with double-stranded RNA. [GOC:jl]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A 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: UDP-N-acetyl-D-glucosamine + beta-D-mannosyl-R = UDP + 4-(N-acetyl-beta-D-glucosaminyl)-beta-D-mannosyl-R. [EC:2.4.1.144]
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]
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]
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]
A protein complex which is capable of GABA-A receptor activity. In human, it is usually composed of either two alpha, two beta and one gamma chain of the GABA-A receptor subunits or 5 chains of the GABA-A receptor subunits rho1-3 (formally known as GABA-C receptor). [GO_REF:0000088, GOC:bhm, GOC:TermGenie, PMID:18790874]
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 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 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 by the binding of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, to a cell surface receptor. [GOC:mah]
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 an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts. [GOC:mtg_transport, ISBN:0815340729]
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
Combining with the amino acid gamma-aminobutyric acid (GABA, 4-aminobutyrate) to initiate a change in cell activity. GABA-A receptors function as chloride channels. [PMID:8974333]
An electron dense body which may contain granules. [ISBN:0195065719, NIF_Subcellular:sao730872736]
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 complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation. [PMID:10749213, PMID:15145345]
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 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 nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. [GOC:dph, GOC:tb]
Any process in which RNA molecules inactivate expression of target genes. [GOC:dph, GOC:mah, GOC:tb, PMID:15020054]
The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [ISBN:0198506732]
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. [CL:0000062, GO_REF:0000034, GOC:jid]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Catalysis of the hydrolysis of ester linkages within nucleic acids. [ISBN:0198547684]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
The 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 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 modulates the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
A series of molecular signals initiated by the binding of nerve growth factor (NGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, PMID:11520933, PR:000011194, Wikipedia:Nerve_growth_factor]
The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. [GOC:go_curators, GOC:mtg_sensu]
Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins. [GOC:go_curators, Pfam:PF00595]
Modulates the activity of a protein kinase, an enzyme which phosphorylates a protein. [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 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 transfer of a specific substance or group of related substances from one side of a membrane to the other. [GOC:jid, GOC:mtg_transport, ISBN:0815340729]
Enables the transfer of a substance from one side of a membrane to the other. [GOC:mtg_transport, ISBN:0815340729]
Enables the 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 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 involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide. [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 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 any of the compartments of the Golgi apparatus. [GOC:mah]
The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:jl]
The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y. [GOC:ai]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sugar(out) + H+(out) = sugar(in) + H+(in). [TC:2.A.1.1.-]
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]
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]
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 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]
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 sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule. [GOC:mah, PMID:22562358]
Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. [GOC:mah, ISBN:0198547684]
Catalysis of the hydrolysis of ester linkages within nucleic acids. [ISBN:0198547684]
Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. [EC:4.2.99.18]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
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 myoblast proliferation. [GOC:BHF]
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 the covalent addition of methyl groups to histones. [GOC:mah]
Any process that modulates the frequency, rate or extent of skeletal muscle satellite cell proliferation. [GOC:ef, GOC:mtg_muscle, PMID:16607119]
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 transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. [GOC:txnOH]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes. [GOC:add, ISBN:068340007X]
Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Catalysis of the reaction: 4 R'C(R)SH + O2 = 2 R'C(R)S-S(R)CR' + 2 H2O. [EC:1.8.3.2]
Catalysis of the formation of disulfide bridges. [PMID:10899311]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds. [MetaCyc:DISULFOXRED-RXN]
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]
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]
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 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 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]
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 that mediates transport between the trans-Golgi network and other parts of the cell. [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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
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 network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination. [GOC:vw, ISBN:0815316194]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
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]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide. [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]
Interacting selectively and non-covalently with a phosphorylated protein. [GOC:ai]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
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]
Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it. [ISBN:0198506732]
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]
An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a. [EC:2.7.11.19]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
The phosphorylation of peptidyl-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 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 of introducing a phosphate group on to a protein. [GOC:hb]
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]
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 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 calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states. [GOC:krc]
Catalysis of the reaction: 4 ATP + 2 phosphorylase b = 4 ADP + phosphorylase a. [EC:2.7.11.19]
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 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 mediates the transfer of information from one cell to another and contributes to the progression of the mammary gland, from its initial state to the mature structure. [GOC:dph]
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]
The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland. [GOC:dph]
Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted. [GOC:dph]
The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus. [GOC:dph, PMID:18824147]
The process in which the anatomical structures of cartilage are generated and organized. [GOC:dph]
The process in which the anatomical structures of cartilage in the trachea are generated and organized. [GOC:dph]
The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung. [GOC:dph, GOC:mtg_lung]
The biological process whose specific outcome is the progression of a lobar bronchus epithelium from an initial condition to its mature state. This process begins with the formation of the lobar bronchus epithelium and ends with the mature structure. The lobar bronchus epithelium is the tissue made up of epithelial cells that lines the inside of the lobar bronchus. [GOC:dph, GOC:mtg_lung]
The process in which a relatively unspecialized cell acquires specialized features of a lung goblet cell. A goblet cell is a cell of the epithelial lining that produces and secretes mucins. [GOC:dph, GOC:mtg_lung]
The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. [GOC:dph, GOC:mtg_lung]
The process in which a trachea is generated and organized. The trachea is the portion of the airway that attaches to the bronchi as it branches. [GOC:dph]
The biological process whose specific outcome is the progression of a bronchiole from an initial condition to its mature state. This process begins with the formation of the bronchiole and ends with the mature structure. A bronchiole is the first airway branch that no longer contains cartilage; it is a branch of the bronchi. [GOC:dph, GOC:mtg_lung]
The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113]
The process 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 whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways. [GOC:mtg_lung, PMID:9751757]
Any process that activates or 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 erythrocyte differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The increase in size or mass of an entire multicellular organism, as opposed to cell growth. [GOC:bf, GOC:curators, GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of mammary gland epithelial cell proliferation. [GOC:mah]
The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone. [GOC:dgh]
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 frequency, rate or extent of angiogenesis. [GOC:go_curators]
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 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]
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 of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. [ISBN:0198506732]
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]
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 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]
A system process carried out by the organs and tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. [GOC:dph, GOC:mtg_cardio, GOC:tb]
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]
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 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 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 protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands. [PMID:17543136]
A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:mah, GOC:signaling]
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
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 part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP. [GOC:dph, GOC:mah, GOC:tb]
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 vesicle fusion. [GOC:mah]
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]
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]
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 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]
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. [GOC:jl, ISBN:0395825172, ISBN:0815316194]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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 transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with 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 monomeric actin, also known as G-actin. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. [GOC:txnOH]
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 any nucleic acid. [GOC:jl]
The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. [GOC:go_curators]
A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732]
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
Any process that modulates the frequency, rate or extent of cytoplasmic translation. [GOC:obol]
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 activates or increases the frequency, rate or extent of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator. [GOC:TermGenie, pubmed:17719541]
A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered. [GOC:mah, GOC:mtg_apoptosis]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a platelet alpha granule. A platelet alpha granule is a secretory organelle found in blood platelets. [GOC:rph, PMID:16123220]
Any process that activates or increases the frequency, rate or extent of adipocyte differentiation. [GOC:go_curators]
The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow. [CL:0000556, GOC:BHF, GOC:vk]
The process in which platelets bud from long processes extended by megakaryocytes. [GOC:mah, ISBN:0815316194]
Any process that modulates the frequency, rate or extent of gene expression after the production of a mRNA transcript by its transport into, or maintainance in, a specific location within the cell. [GOC:dph, GOC:tb]
Any process in which mRNA is transported to, or maintained in, a specific location within the cell. [GOC:ai]
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 acquisition and processing of information and/or the storage and retrieval of this information over time. [GOC:jid, PMID:8938125]
The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. [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 a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
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 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]
Interacting selectively and non-covalently with one of the p53 family of proteins. [GOC:hjd]
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 cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
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 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 in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. [GOC:jl]
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]
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 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 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 double-strand break repair via nonhomologous end joining. [GOC:obol]
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. [GOC:BHF, GOC:mah]
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 process that activates or increases the frequency, rate or extent of isotype switching to IgA isotypes. [GOC:jid]
The modification of histone H4 by addition of one or more methyl groups to lysine at position 20 of the histone. [GOC:mah]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone. [GOC:pr, GOC:tb]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The process in which anatomical structure of an atrial septum secundum is generated and organized. [GOC:mtg_heart]
The process in which anatomical structure of an atrial septum primum is generated and organized. [GOC:mtg_heart]
The process in which the membranous septum is generated and organized. The membranous septum is the upper part of ventricular septum. [GOC:mtg_heart]
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 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]
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]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the transfer of a methyl group to an acceptor molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with 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]
The modification of a histone by addition of one or more methyl groups to a lysine residue. [GOC:mah, GOC:pr]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The modification, often by sulfation, of sugars incorporated into heparan sulfate after polymerization. [ISBN:0815316194]
Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + heparan sulfate = adenosine 3',5'-bisphosphate + heparan sulfate 6-O-sulfate; results in 6-O-sulfation of glucosamine residues in heparan sulfate. [PMID:8631808]
Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate. [EC:2.8.2, GOC:curators]
The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle. [CHEBI:45931, GOC:jl, ISBN:0140512713]
The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver. [CHEBI:18385, GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver. [GOC:mlg]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: ATP + thiamine = AMP + thiamine diphosphate. [EC:2.7.6.2]
A protein complex between the ATPase VCP (p97) and its cofactor p47 (NSFL1C). In human, the protein complex consists of one homotrimer of NSFL1C/p47 per homohexamer of VCP/p97. [GOC:bf, GOC:PARL, PMID:9214505]
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 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 electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system. [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]
A protein complex 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]
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]
A multiprotein ATPase complex required for the efficient dislocation of ER-lumenal degradation substrates, and their subsequent proteolysis by the proteasome. In budding yeast, this complex includes Cdc48p, Npl4p and Ufd1p proteins. In mammals, this complex includes a hexamer of VCP/p97 (a cytosolic ATPase) and trimers of each of its cofactors UFD1L and NPL4 (NPLOC4) (e.g. a 6:3:3 stoichiometry). [PMID:11813000, PMID:16179952]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. [GOC:mah, GOC:tb]
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]
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 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 ATP biosynthetic process. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of ubiquitin-specific protease (deubiquitinase) activity. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of oxidative phosphorylation. [GO_REF:0000058, GOC:TermGenie, PMID:10225962]
Any process that modulates the frequency, rate or extent of aerobic respiration. [GO_REF:0000058, GOC:TermGenie, PMID:19266076]
Any process that activates or increases the frequency, rate or extent of Lys63-specific deubiquitinase activity. [GO_REF:0000059, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22970133]
Any process that activates or increases the frequency, rate or extent of protein K63-linked deubiquitination. [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22970133]
The process in which autophagosomes, double-membraned vacuoles containing cytoplasmic material fuse with a vacuole (yeast) or lysosome (e.g. mammals and insects). In the case of yeast, inner membrane-bounded structures (autophagic bodies) appear in the vacuole. Fusion provides an acidic environment and digestive function to the interior of the autophagosome. [GOC:autophagy, GOC:lf, PMID:11099404, PMID:16874026, PMID:17534139]
The chemical reactions and pathways resulting in the breakdown of flavin adenine dinucleotide, which acts as a coenzyme or prosthetic group of various flavoprotein oxidoreductase enzymes. [CHEBI:24040, 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 aggregation, arrangement and bonding together of a set of components to form an aggresome; requires the microtubule cytoskeleton and dynein. [GOC:BHF, GOC:rl, PMID:14675537]
The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GOC:go_curators]
The 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 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]
The formation of a protein hexamer, a macromolecular structure consisting of six noncovalently associated identical or nonidentical subunits. [GOC:ecd]
Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of protein complex assembly. [GOC:mah]
The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon. [PMID:11994744]
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 replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide. [GOC:elh, GOC:vw, PMID:10535901]
Any process involved directly in viral genome replication, including viral nucleotide metabolism. [ISBN:0781702534]
The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification. [GOC:jsg, RESID:AA0151, RESID:AA0420, RESID:AA0421]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of establishment or extent of a mitochondrial membrane potential, the electric potential existing across any mitochondrial membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:dph, GOC:tb]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. [GOC:go_curators]
Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process. [GOC:al, GOC:dph, GOC:jl, GOC:mtg_apoptosis, GOC:tb, PMID:14744432, PMID:18328827, Wikipedia:Caspase]
The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation. [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:9412464]
The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid. [GOC:jl, ISBN:0618254153]
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 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 with a ubiquitin-specific protease. [GOC:bf, GOC:PARL, PMID:24063750]
Interacting selectively and non-covalently with a BAT3 complex. [GO_REF:000102, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:23246001]
Interacting selectively and non-covalently with a ubiquitin-like protein ligase, such as ubiquitin-ligase. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with major histocompatibility complex class I 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 and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers. [GOC:al, PMID:20739285]
Increases the activity of deubiquitinase, an enzyme that catalyzes the hydrolysis of various forms of polymeric ubiquitin sequences. [GOC:sart, ISBN:0120793709]
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 polymer of ubiqutin. [GOC:mah]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
Interacting selectively and non-covalently with any protein phosphatase. [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]
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 an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A 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]
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]
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 lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2). [GOC:mtg_sensu, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The directed movement of hydrogen ion (proton) across a membrane. [GO_REF:0000069, GOC:pr, GOC:TermGenie]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor. [GOC:das, GOC:jl, ISBN:0140513590]
The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV. [ISBN:0716731363]
Binds to and modulates the activity of an enzyme. [GOC:dph, GOC:mah, GOC:tb]
Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O. [EC:1.9.3.1]
Any process that modulates 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]
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 IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate. [GOC:mah, ISBN:0716720094]
Catalysis of the reaction: N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + ATP + H(2)O = 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate + ADP + 2 H(+) + phosphate. [EC:6.3.5.3, RHEA:17132]
A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. [http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm, ISBN:0198506732]
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. [GOC:mah, GOC:vw]
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]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
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 in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. [GOC:jl]
An oxidoreductase complex which is capable of GMP reductase activity. It catalyses the irreversible reaction: GMP + 2 H(+) + NADPH => IMP + NADP(+) + NH(4)(+). [GOC:bhm, GOC:TermGenie, PMID:12009299]
A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates). [GOC:ma]
The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. [GOC:go_curators, ISBN:0198506732]
The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine. [CHEBI:26386, GOC:go_curators]
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]
Catalysis of the reaction: IMP + NADP(+) + NH(4)(+) = GMP + 2 H(+) + NADPH. [EC:1.7.1.7, RHEA:17188]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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 an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far. [GOC:mah, PR:000000017]
Any process that 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 increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter. [GOC:dph, GOC:tb, 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 in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction. [GOC:jl, GOC:pamgo_curators]
Reactions triggered in response to the presence of a protozoan that act to protect the cell or organism. [GOC:jl]
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. [GOC:jl]
Any process that activates or increases the frequency, rate, or extent of interleukin-12 production. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. [GOC:add, GOC:mah]
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. [GOC:add, ISBN:0781735149]
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 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]
An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. [ISBN:0198506732]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
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 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]
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. [GOC:txnOH]
Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. [GOC:txnOH]
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 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 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]
A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. [GOC:elh]
The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA. [GOC:mah]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. [GOC:jl, PMID:11584301]
The lipid bilayer surrounding a multivesicular body. [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]
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 developmental process that results in the deposition of coloring matter in an organism, tissue or cell. [ISBN:0582227089]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a melanosome. A melanosome is a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. [GOC:vk]
The portion of the photoreceptor cell cilium linking the photoreceptor inner and outer segments. It's considered to be equivalent to the ciliary transition zone. [GOC:cilia, PMID:15917207, PMID:22653444, PMID:8718680]
The 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 outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes. [GOC:cilia, ISBN:0824072820]
The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. [GOC:bf, GOC:dph, ISBN:0815340729]
Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light. [CL:0000210, GOC:bf, GOC:rl]
Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. [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 assembly and organization of an axoneme, 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, GOC:jl, ISBN:0815316194]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GOC:vw, ISBN:0198506732]
A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. [http://www.cellnucleus.com/]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure. [GOC:mtg_heart]
The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body. [GOC:bf, GOC:dgh, MA:0000062, UBERON:0000947, Wikipedia:Aorta]
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]
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 progression of a cardiac septum over time, from its initial formation to the mature structure. [GOC:mtg_heart]
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 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 initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK). [PMID:9561267]
Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [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 part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. [GOC:jl, ISBN:0395825172]
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]
Completion of folding of alpha- and beta-tubulin; takes place subsequent to chaperonin-mediated partial folding; mediated by a complex of folding cofactors. [PMID:10542094]
The aggregation and bonding together of alpha- and beta-tubulin to form a tubulin heterodimer. [GOC:mah]
Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin. [GOC:krc]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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]
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 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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
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]
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 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]
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 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 activates or increases the frequency, rate or extent of adipocyte differentiation. [GOC:go_curators]
The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. [ISBN:0716731185]
Any process that activates or increases the frequency, rate or extent of cell migration. [GOC:go_curators]
The process in which a relatively unspecialized cell acquires specialized features of a neuron. [GOC:mah]
The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state. [GOC:dph, GOC:go_curators, PMID:11532397]
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 process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage. [GOC:dph]
Interacting selectively and non-covalently with the frizzled (fz) receptor. [GOC:ceb, PR:000001315]
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 structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. [GOC:mah, ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Stops, prevents or reduces the activity of a calcium-dependent protein kinase. [GOC:mah]
Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
A hexameric protein complex required for the initiation and regulation of DNA replication. [GOC:jl, PMID:11282021]
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]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action. [ISBN:071673706X, ISBN:0815316194]
The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication. [ISBN:071673706X, ISBN:0815316194]
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. [GOC:mah]
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 the DNA helix. [EC:3.6.1.3, GOC:jl]
Interacting selectively and non-covalently with single-stranded DNA. [GOC:elh, GOC:vw, PMID:22976174]
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 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 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 component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential. [GOC:mah]
A process in which a potassium ion is transported from one side of a membrane to the other. [GOC:mah]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer. [GOC:ai]
Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. [GOC:mah]
The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
Enables the transmembrane transfer of a potassium ion by an outwardly-rectifying voltage-gated channel that produces a transient outward current upon a step change in membrane potential. [GOC:mah, PMID:5575340]
Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0815340729]
Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
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]
A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin G (IgG) to an Fc-gamma receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region. [GOC:phg, PMID:11244038]
The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. [GOC:add, ISBN:0781735149]
An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, 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 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 protein complex capable of catalyzing 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). [GOC:bhm, PMID:16540464]
The dense fibrillar network lying on the inner side of the nuclear membrane. [ISBN:0582227089]
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 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 keratinocyte apoptotic process. [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, GOC:TermGenie, PMID:18938133]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of the addition of SUMO groups to a protein. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB. [GOC:dph, GOC:rl, GOC:tb]
The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein. [GOC:jl, PMID:11265250]
Any process that decreases the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor. [GOC:dph, GOC:tb]
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 SUMO to a substrate protein via the reaction X-SUMO + S --> X + S-SUMO, where X is either an E2 or E3 enzyme, the X-SUMO linkage is a thioester bond, and the S-SUMO linkage is an isopeptide bond between the C-terminal amino acid of SUMO and the epsilon-amino group of lysine residues in the substrate. [GOC:dph]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages. [GOC:rn, PMID:11031248, PMID:11265250]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
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 the pre-autophagosomal structure 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:mf]
The component of the omegasome 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:mf, PMID:18725538, PMID:24591649]
A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. [GOC:go_curators, ISBN:0198506732]
A zone of apposition between endoplasmic-reticulum and mitochondrial membranes, structured by bridging complexes. These contact sites are thought to facilitate inter-organelle calcium and phospholipid exchange. [GOC:jl, PMID:19556461]
A phosphatidylinositol 3-kinase complex that contains a catalytic class III phosphoinositide 3-kinase (PI3K) subunit bound to a regulatory (adaptor) subunit. Additional adaptor proteins may be present. Class III PI3Ks have a substrate specificity restricted to phosphatidylinositol (PI). [GOC:bf, PMID:9255069]
A cellular membrane associated with the pre-autophagosomal structure. [GOC:mah, GOC:rph, PMID:16874040, PMID:17382324]
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]
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]
The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential. [GOC:PARL, PMID:18200046, PMID:23985961]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving triglyceride, any triester of glycerol. [GOC:dph, GOC:sl, GOC:tb]
Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity. [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 deprivation of glucose. [GOC:jl]
The initial attachment of an autophagosome membrane to the target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane. Docking requires only that the two membranes come close enough for these proteins to interact and adhere. [GOC:autophagy, GOC:mah]
The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure.  Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded. [PMID:11099404, PMID:12914914, PMID:15798367, PMID:16973210, PMID:20159618, PMID:9412464]
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. [GOC:dph, GOC:tb]
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]
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 directed movement of substances from endosomes to lysosomes. [GOC:ai, ISBN:0716731363]
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]
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 rate of addition of phosphate groups to amino acids within a protein. [GOC:hjd]
Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. [GOC:hjd]
The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm. [GOC:autophagy, PMID:9412464]
The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
A 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 chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. [CHEBI:50860, GOC:mah]
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]
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 phosphate group from one position to another within a single molecule. [GOC:mah]
Catalysis of the reaction: D-ribose 1-phosphate = D-ribose 5-phosphate. [EC:5.4.2.7]
Catalysis of the reaction: alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate. [EC:5.4.2.2]
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]
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 reactive oxygen species metabolic process. [GOC:mah]
Any process that stops, prevents or reduces the frequency, rate or extent of ATP metabolic process. [GO_REF:0000058, GOC:TermGenie, PMID:20695849]
Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrion degradation (mitophagy). [GO_REF:0000058, GOC:autophagy, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24600391]
Any process in which a protein is maintained in a specific location in a mitochondrion, and is prevented from moving elsewhere. [GOC:mah]
The directed movement of a protein to the mitochondrion or a part of the mitochondrion. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein. [GOC:mah]
Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. [GOC:dph, GOC:tb]
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]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with 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]
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 protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex. [GOC:jh2, PMID:9529603]
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 activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome. [GOC:mah]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues. [GOC:BioGRID, GOC:dph, GOC:mah, GOC:tb, PMID:22863777]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins. [GOC:vp]
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 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 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 conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa. [PMID:9242902]
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 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 signal transduction process that contributes to a DNA damage checkpoint. [GOC:mah]
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. [ISBN:0198506732]
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 WD40 repeat domain of a protein. The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Several of these repeats are combined to form a type of protein domain called the WD domain. [GOC:yaf, InterPro:IPR017986]
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 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 function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II. [GOC:txnOH, PMID:16858867]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH]
A enzyme complex of which the core is a heterodimer composed of a light (alpha) and heavy (beta) chain, and requires several other water-soluble proteins of cytosolic origin for activity. Functions in superoxide generation by the NADPH-dependent reduction of O2. [GOC:jl, PMID:11483596, PMID:12440767]
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 metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
Any process that activates or increases the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
A process that results in the breakdown of the extracellular matrix. [GOC:jid]
The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species. [CHEBI:18421, GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [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 any enzyme. [GOC:jl]
Increases the activity of the enzyme superoxide-generating NADPH oxidase. [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]
An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane. [GOC:dph, GOC:jid, GOC:kmv, GOC:rph, PMID:10930469, PMID:15601896, PMID:16246101, PMID:21556374, PMID:21562044]
A 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]
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 membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins. [PMID:23563491]
Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells. [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]
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]
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 neuron migration. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of male gonad development. [GOC:obol]
The process whose specific outcome is the progression of an acoustico-facial VII-VIII ganglion complex over time, from its formation to the mature structure. [GO_REF:0000094, GOC:bf, GOC:mat, GOC:PARL, GOC:TermGenie, PMID:18356247]
Any neural crest cell migration that is involved in sympathetic nervous system development. [GO_REF:0000060, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:19325129]
Any semaphorin-plexin signaling pathway that is involved in axon guidance. [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:22790009]
Any semaphorin-plexin signaling pathway that is involved in neuron projection guidance. [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:22790009]
Any neural crest cell migration that is involved in autonomic nervous system development. [GOC:BHF, GOC:TermGenie]
The process in which the migration of a sympathetic neuron projection is directed to a specific target site in response to a combination of attractive and repulsive cues. [GOC:BHF, GOC:rl, PMID:22790009]
Long distance growth of a single sympathetic neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:BHF, GOC:rl, PMID:22790009]
A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand. [GOC:BHF, GOC:mah, GOC:vk, PMID:15239959]
The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure. [GOC:dph]
The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure. [GOC:BHF, GOC:rl]
The process in which a salivary epithelial cord bifurcates at its end. [GOC:dph]
The neurite development process that generates a long process of a neuron, as it invades a target tissue. [GOC:dph, GOC:sart]
The directed movement of a motile cell or organism towards a lower concentration of a chemical. [GOC:ai, GOC:bf, GOC:isa_complete]
The long distance growth of a single cell process, that is involved in the migration of an axon growth cone, where the migration is directed to a specific target site by a combination of attractive and repulsive cues. [GOC:ef, GOC:jid]
Any process that stops, prevents, or reduces the frequency, rate or extent of axon extension involved in axon guidance. [GOC:devbiol]
Any process that modulates the frequency, rate or extent of axon extension involved in axon guidance. [GOC:devbiol]
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]
The movement of trunk neural crest cells from the neural tube, travelling ventrally through the anterior half of each sclerotome. Trunk neural crest cells that remain in the sclerotome form the dorsal root ganglia containing the sensory neurons. Trunk neural crest cells that continue more ventrally form the sympathetic ganglia, the adrenal medulla, and the nerve clusters surrounding the aorta. [GOC:bf, GOC:mat, GOC:PARL, PMID:16319111, PMID:19386662]
Any process that stops, prevents, or reduces the frequency, rate or extent of axon outgrowth. [GOC:mah]
The directional movement of a gonadotrophin-releasing hormone producing neuron from the nasal placode to the hypothalamus. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The process in which a branchiomotor neuron growth cone is directed to a specific target site. Branchiomotor neurons are located in the hindbrain and innervate branchial arch-derived muscles that control jaw movements, facial expression, the larynx, and the pharynx. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:14699587]
The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process that contributes to the act of creating the structural organization of the oculomotor nerve. This process pertains to the physical shaping of a rudimentary structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The process that contributes to the act of creating the structural organization of the facial nerve. This process pertains to the physical shaping of a rudimentary structure. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
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 stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration. [GOC:BHF, GOC:dph, GOC:tb]
The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues. [CL:0000100, GOC:pr, ISBN:0878932437]
The collection of axons into a bundle of rods, known as a fascicle. [GOC:dgh]
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]
Any process that modulates the frequency or rate of heart contraction. [GOC:dph, GOC:tb, PMID:10358008]
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]
Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal. [GOC:ai]
Interacting selectively and non-covalently with a member of the neuropilin family. [GOC:bf, PMID:23871893]
Interacting selectively and non-covalently with semaphorin receptors. [GOC:ceb, PMID:12001990]
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]
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 RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
The 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 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]
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 irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
Any process that increases the concentration of calcium ions in mitochondria. [GOC:ai]
Any process that decreases the concentration of calcium ions in the endoplasmic reticulum. [GOC:mah]
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 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 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]
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 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 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]
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 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 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 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 any metal ion. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. [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 complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. [GOC:elh]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
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 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 protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2). [GOC:mtg_sensu, ISBN:0198547684]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
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 hydrogen ion (proton) across a membrane. [GO_REF:0000069, GOC:pr, GOC:TermGenie]
The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV. [ISBN:0716731363]
Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O. [EC:1.9.3.1]
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]
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 lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. [GOC:go_curators]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [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 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: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate. [EC:3.1.4.46]
Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. [EC:3.1.4, GOC:curators]
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]
The component of the nuclear inner membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:go_curators]
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 metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. [GOC:go_curators]
Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain. [GOC:BHF, GOC:vk, InterPro:IPR008251, PMID:7667093]
Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP. [GOC:jl]
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]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
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]
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. [ISBN:0198506732]
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. [GOC:dgh]
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]
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 regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery. [GOC:txnOH, PMID:10213677, PMID:16858867]
Interacting selectively and non-covalently with a 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 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 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]
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]
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 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 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 GTP, guanosine triphosphate. [GOC:ai]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A 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]
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 myoblast proliferation. [GOC:BHF]
A cell cycle process that activates or increases the rate or extent of the transition from the G0 quiescent state to the G1 phase. [GOC:mah]
The process whose specific outcome is the progression of the myoblast over time, from its formation to the mature structure. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. [CL:0000056, GOC:dph, GOC:mtg_muscle]
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 striated muscle development. [GOC:go_curators]
The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage. [GOC:ef, GOC:mtg_muscle, PMID:12021255, PMID:16607119]
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]
Any process that activates, maintains or increases the frequency, rate or extent of activation of satellite cell involved in skeletal muscle regeneration. The activation of satellite cell is the process that initiates satellite cell division by causing it to move from quiescence to the G1 stage of the cell cycle. The cell swells and there are a number of other small changes. The cells then start to divide. Following cell division the cells will differentiate. [GOC:mtg_muscle]
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 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 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 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]
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. [GOC:bf, GOC:cilia, ISBN:0198547684]
Any of the 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 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]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The hydrolysis of 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]
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]
Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide. [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]
Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. [GOC:jl, PMID:17152095]
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 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]
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 pertaining to the functions of the nervous and muscular systems of an organism. [GOC:ai]
Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors. [GOC:ai, GOC:dph, http://www.onelook.com/]
The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. [GOC:kmv, GOC:mtg_sensu, GOC:pr]
Any process that 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 a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. [GOC:jl]
The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord. [CL:0000127, GOC:go_curators]
The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier. [GOC:dgh, GOC:mah]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. [GOC:mah]
The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties. [ISBN:0192800981]
A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. [GOC:jl, http://en.wikipedia.org/wiki/Sexual_reproduction, ISBN:0387520546]
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:dph, GOC:mah, GOC:tb, PMID:11102830]
The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages. [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]
Any process that modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
The behavior of a male, for the purpose of attracting a sexual partner. An example of this process is found in Drosophila melanogaster. [GOC:mtg_sensu, GOC:pr]
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GOC:dph]
The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. [GOC:ai]
The infiltration by sperm of the zona pellucida to reach the oocyte. The process involves digestive enzymes from a modified lysosome called the acrosome, situated at the head of the sperm. [GOC:jl, http://arbl.cvmbs.colostate.edu/hbooks/pathphys/reprod/fert/fert.html]
The union of male and female gametes to form a zygote. [GOC:ems, GOC:mtg_sensu]
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]
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. [GOC:ceb, GOC:mah]
The chemical reactions and pathways resulting in the breakdown of ganglioside, a ceramide oligosaccharide carrying, in addition to other sugar residues, one or more sialic residues. [ISBN:0198547684]
The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide. [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]
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 nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [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 transfer of an N-acetylglucosaminyl residue from UDP-N-acetyl-glucosamine to a sugar. [ISBN:0198506732]
Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. [EC:3.2.1.52]
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 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]
Generation of a long process of a pyramidal cell, that carries efferent (outgoing) action potentials from the cell body in cerebral cortex layer V towards target cells in the gray matter of the spinal cord. This axonal process is a member of those that make up the corticospinal tract. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:9878731]
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 protein complex that has aspartic-type endopeptidase activity, and contains a catalytic subunit, presenilin (PS), that is a prototypical member of the GxGD-type aspartyl peptidases. The complex also contains additional subunits, including nicastrin, APH-1, PEN-2, and a regulatory subunit, CD147. Gamma-secretase cleaves several transmembrane proteins including the cell surface receptor Notch and the beta-amyloid precursor protein. [GOC:mah, PMID:15286082, PMID:15890777, PMID:17047368]
Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. [GOC:mah, PMID:22160157]
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 irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
Any process that activates or increases the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
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 series of successive proteolytic cleavages of the Notch protein, which result in an active form of the receptor. [PMID:12651094, PMID:14986688]
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]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. [http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
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]
The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster. [GOC:jl, GOC:mah, GOC:pde, GOC:vw]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [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]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
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 series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand. [GOC:BHF, GOC:mah, GOC:vk, PMID:15239959]
The process in which a relatively unspecialized cell acquires specialized features of a muscle cell. [CL:0000187, GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade. [GOC:mah]
The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The orderly movement of a cell that will reside in the hindbrain. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
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]
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]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. [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]
A two-stranded helical polymer of the protein actin. [GOC:mah]
A vesicle found in the cytoplasm of a cell. [GOC:ai, GOC:mah, GOC:vesicles]
A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters. [GOC:jl, GOC:krc, PMID:16858867, Wikipedia:Rna_polymerase_ii]
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]
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]
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]
Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork. [ISBN:0124325653]
Any process that modulates the frequency, rate or extent of 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 transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage. [GOC:go_curators]
A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. [GOC:mah, ISBN:0198506732, ISBN:0716731363]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion. [GOC:bf]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
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]
A synapse in which an action potential in the presynaptic cell reduces the probability of an action potential occurring in the postsynaptic cell. [GOC:dph, GOC:ef]
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]
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 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 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 leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
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]
Any process that activates or increases the frequency, rate or extent of the acrosome reaction. [GOC:obol]
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 or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an alcohol stimulus. [CHEBI:30879, 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 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 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]
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]
A reflex process in which an animal immediately tries to turn over after being placed in a supine position. [GOC:dph, PMID:8635460]
The process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine. [GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. [GOC:ai]
Any process pertaining to the functions of the nervous and muscular systems of an organism. [GOC:ai]
Any process in which an organism voluntarily modulates its posture, the alignment of its anatomical parts. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment. [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 amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. [CHEBI:33709, GOC:ef, GOC:mlg]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg. [GOC:jid, GOC:pr, ISBN:0198606907]
The 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 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]
The vesicular release of classical neurotransmitter molecules from a neuron, across a chemical synapse, the subsequent activation of neurotransmitter receptors of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. [GOC:jl, MeSH:D009435]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. [GOC:ef, GOC:mtg_muscle, ISBN:0198506732]
The directed movement of 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]
A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates. [GOC:dph, GOC:tb, PMID:12458206]
An action or movement due to the application of a sudden unexpected stimulus. [GOC:dph]
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8]
Interacting selectively and non-covalently with taurine. [GOC:mlg]
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]
Interacting selectively and non-covalently with zinc (Zn) ions. [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 living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
Any process that activates or increases the frequency, rate or extent of signal transduction. [GOC:sm]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell. [GOC:bf, GOC:signaling, PMID:11790549, PMID:20811974]
Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:kd, GOC:mah]
Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68). [GOC:mah, GOC:so]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Catalysis of the transfer of a methyl group to an acceptor molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds. [GOC:jl]
Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:dph, GOC:tb]
A protein complex that possesses activity that prevents or downregulates transcription. [GOC:mah]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
A second wave of blood cell production that, in vertebrates, generates long-term hemopoietic stem cells that continously provide erythroid, myeloid and lymphoid lineages throughout adulthood. [GOC:bf, GOC:dph, PMID:15378083, PMID:15617691]
A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. [GOC:dph]
The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113]
The process in which the anatomical structures of the eye are generated and organized during embryonic development. [GOC:jid, GOC:mtg_sensu]
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 in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus. [GOC:go_curators]
The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. [GOC:ecd, http://life.nthu.edu.tw/~g864204/dict-search1.htm]
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. [GOC:jid, UBERON:0002048]
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. [GOC:mah]
The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. [GOC:mah]
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. [GOC:mah]
The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. [GO_REF:0000022, GOC:jid, GOC:mah, GOC:mtg_15nov05]
The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. [GO_REF:0000022, GOC:mah, GOC:mtg_15nov05]
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 embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin. [GOC:add, ISBN:068340007X]
The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes. [GOC:add, ISBN:068340007X]
The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell. [GOC:dph, ISBN:0124020607, ISBN:0198542771]
The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell. [GOC:add, ISBN:0781735149]
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 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]
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 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]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to 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 the core promoter. The transcribed region might be described as a gene, cistron, or operon. [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 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]
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 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]
The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue. [GOC:go_curators, ISBN:0198506732]
Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication. [GOC:add, GOC:dph, GOC:tb, ISBN:0781735149]
Any 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]
Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic GMP-AMP. [GOC:dph, PMID:23258413]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
A small membrane-bounded vesicle that releases its contents by exocytosis in response to insulin stimulation; the contents are enriched in GLUT4, IRAP and VAMP2. [PMID:17644329]
Any small, fluid-filled, spherical organelle enclosed by membrane. [GOC:mah, GOC:pz, GOC:vesicles]
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]
Any process that modulates the frequency, rate or extent of endocytosis. [GOC:go_curators]
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]
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate. [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 GTP, guanosine triphosphate. [GOC:ai]
Catalysis of the reaction: GTP + H2O = GDP + phosphate. [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 cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a large ribosomal subunit; includes transport to the sites of protein synthesis. [GOC:jl]
The directed movement of a protein from the cytoplasm to the nucleus. [GOC:jl]
Interacting selectively and non-covalently with an unfolded protein. [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 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 rhythm of the locomotor activity of an organism during its 24 hour activity cycle. [GOC:go_curators]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
Interacting selectively and non-covalently with a G-protein coupled receptor. [GOC:ceb, GOC:dph]
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]
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]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [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]
Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell apoptotic process. [GO_REF:0000058, GOC:TermGenie, PMID:19137015]
The morphogenetic growth of the large, club-shaped terminal end of a mammary gland duct during prepubertal growth and during puberty. [GOC:dph, PMID:10804170]
Any process that modulates the frequency, rate or extent of the JAK-STAT signaling pathway. [GOC:bf]
Any process that activates or increases the rate or extent of mammary gland epithelial cell proliferation. [GOC:mah]
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 modulates the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus. [GOC:BHF, GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Attachment of the blastocyst to the uterine lining. [GOC:isa_complete, http://www.medterms.com]
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 internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
A 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 process in which a uridine in position 34 of a mitochondrial tRNA is post-transcriptionally modified. [GOC:mah, GOC:mcc]
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 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]
The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified. [GOC:hjd, ISBN:155581073X]
Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Catalysis of an oxidation-reduction (redox) reaction, 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 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]
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 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/]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A 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]
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 pri-miRNA transcription from RNA polymerase II promoter. [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure. [GOC:mtg_heart]
Any process that decreases 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:BHF, GOC:dph, GOC:tb]
The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. [CL:0000136, GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body. [GOC:bf, GOC:dgh, MA:0000062, UBERON:0000947, Wikipedia:Aorta]
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 laminar fluid shear stress stimulus. Laminar fluid flow is the force acting on an object in a system where the fluid is moving across a solid surface in parallel layers. As an example, laminar shear stress can be seen where blood flows against the luminal side of blood vessel walls. [GOC:ecd]
The attachment of a cell to the underlying substrate via adhesion molecules. [GOC:mah, GOC:pf]
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 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 or extent of bone formation. [GOC:go_curators]
Any process that decreases the rate, frequency, or extent of SMAD protein complex assembly. SMAD protein complex assembly is the aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins. [GOC:BHF, GOC:dph, GOC:tb]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
The specification of the dorsal/ventral axis of the embryo, through the products of genes expressed in the zygote. [GOC:bf]
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 immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
Any process 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 ventricular septum over time from its formation to the mature structure. [GOC:mtg_heart]
The process in which the structure of the pulmonary valve is generated and organized. [GOC:mtg_heart]
The process in which the structure of the mitral valve is generated and organized. [GOC:mtg_heart]
The progression of a heart valve over time, from its formation to the mature structure. A heart valve is a structure that restricts the flow of blood to different regions of the heart and forms from an endocardial cushion. [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 ureteric bud over time, from its formation to the mature structure. [GOC:go_curators]
Interacting selectively and non-covalently with a type I activin receptor. [GOC:BHF, GOC:vk]
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 common mediator SMAD signaling protein. [GOC:BHF, GOC:vk, PMID:19114992]
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 an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with a type I transforming growth factor beta receptor. [GOC:BHF, GOC:mah]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
A TGF-beta cytoplasmic mediator that inhibits the signaling function of common-partner and pathway-specific mediators. [PMID:9759503]
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 cis with and relatively close to a core promoter for RNA polymerase II. [GOC:txnOH]
A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome. [PMID:11019806, PMID:12186635, PMID:14570571]
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 activates or increases 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 initiates the activity of an inactive GTPase through the replacement of GDP by GTP. [GOC:dph, GOC:mah, GOC:tb]
The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system. [GOC:bf, GOC:mtg_sensu]
Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine. [GOC:mah]
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]
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]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. [GOC:mah]
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]
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 living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein. [PMID:16792691, PMID:18223036, PMID:18552200]
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/]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
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]
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 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 chemical reactions and pathways involving GDP, guanosine 5'-diphosphate. [GOC:ai]
The chemical reactions and pathways involving GMP, guanosine monophosphate. [GOC:go_curators]
The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. [GOC:go_curators, ISBN:0198506732]
Catalysis of the reaction: ATP + GMP = ADP + GDP. [EC:2.7.4.8]
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 cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a large ribosomal subunit; includes transport to the sites of protein synthesis. [GOC:jl]
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. [GOC:curators]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
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 small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. [GOC:go_curators]
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 part of the larger ribosomal subunit. [GOC:go_curators]
Interacting selectively and non-covalently with any part of a ribosome. [GOC:go_curators]
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 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 GTP, guanosine triphosphate. [GOC:ai]
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]
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 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 multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. [ISBN:0198506732, NIF_Subcellular:sao1038025871]
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 the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
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 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]
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 transfer, from NAD, of ADP-ribose to protein amino acids. [GOC:pr, RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295]
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(P)+ + L-arginine = nicotinamide + N2-(ADP-D-ribosyl)-L-arginine. [EC:2.4.2.31]
Catalysis of the reaction: NAD+ + H2O = nicotinamide + ADP-ribose. [GOC:dph, GOC:pad, GOC:PARL, GOC:pde, PMID:11866528, PMID:7805847]
Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor. [EC:2.4.2.30]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate. [GOC:mah, ISBN:0716720094]
The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. [GOC:go_curators, ISBN:0198506732]
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]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate. [EC:6.3.2.6, RHEA:22631]
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]
Complex that possesses guanylate cyclase activity and is not bound to a membrane. [GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
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 or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. [GOC:lr]
The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue. [GOC:go_curators, ISBN:0198506732]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The process of introducing a phosphate group on to a protein. [GOC:hb]
The chemical reactions and pathways resulting in the formation of cyclic GMP, guanosine 3',5'-phosphate. [ISBN:0198506732]
Catalysis of the cleavage of a phosphorus-oxygen bond 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 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]
Catalysis of the reaction: GTP = 3',5'-cyclic GMP + diphosphate. [EC:4.6.1.2]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds. [GOC:jl]
Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:dph, GOC:tb]
Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it. [GOC:dph, GOC:jl]
The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released. [GOC:jl, http://synapses.mcg.edu/anatomy/chemical/synapse.stm]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate. [GOC:kmv]
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 cold stimulus, a temperature stimulus below the optimal temperature for that organism. [GOC:lr]
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 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]
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]
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]
A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core. [GOC:rb, http://en.wikipedia.org/wiki/Proteasome]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
Any process that modulates 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, GOC:jl]
Binds to and modulates the activity of an enzyme. [GOC:dph, GOC:mah, GOC:tb]
Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. [GOC:mah, PMID:22160157]
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 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 cell motility. [GOC:mah]
Any process that stops, prevents or reduces the frequency, rate or extent of substrate adhesion-dependent cell spreading. [GOC:TermGenie, GOC:yaf]
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]
Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. [GOC:mah]
Any process that modulates the frequency, rate or extent of actin nucleation mediated by the Arp2/3 complex and interacting proteins. [GOC:mah]
Any process that stops, prevents, or reduces the rate of receptor recycling. [GOC:add]
Interacting selectively and non-covalently with the AP-1 adaptor complex. The AP-1 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of beta1, gamma, mu1 and sigma1 subunits and links clathrin to the membrane surface of a vesicle. In at least humans, the AP-1 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (gamma1 and gamma2, mu1A and mu1B, and sigma1A, sigma1B and sigma1C). [PMID:21097499]
Interacting selectively and non-covalently 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]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The directed movement of hydrogen ion (proton) across a membrane. [GO_REF:0000069, GOC:pr, GOC:TermGenie]
Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O. [EC:1.9.3.1]
A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs. [GOC:ab, GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393, PMID:18322460, PMID:19239890]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GOC:go_curators, GOC:rb]
The modification of a protein by cis-trans isomerization of a proline residue. [GOC:krc, PMID:16959570]
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. [ISBN:0198506732]
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]
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 endothelial cell apoptotic process. [GOC:BHF, GOC:mah, GOC:mtg_apoptosis]
The developmental process in which an anatomical stucture is destroyed as a part of its normal progression. [GOC:dph]
The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes. [GOC:add, ISBN:068340007X, ISBN:0781735149]
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 activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
Interacting selectively and non-covalently with a component of the extracellular matrix. [GOC:ai]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
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]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that stops, prevents or reduces the frequency, rate or extent of double-strand break repair. [GOC:BHF]
Any process that stops, prevents or reduces the frequency, rate or extent of histone H2A K63-linked ubiquitination. [GOC:TermGenie]
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 series of molecular signals generated as a consequence of a progesterone binding to its receptor. [GOC:ai, GOC:mah, PMID:14744870]
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]
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 process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
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 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]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation. [GOC:ecd]
Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue. [GOC:mah, GOC:mcc, PMID:10089879, PMID:17190603]
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]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A cilium which may have a variable array of axonemal microtubules but does not contain molecular motors. [GOC:cilia, GOC:dgh, GOC:kmv, PMID:17009929, PMID:20144998, PMID:22118931]
The portion of the plasma membrane surrounding a cilium. [GOC:cilia, GOC:dph, GOC:rph]
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]
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 glial cell-derived neurotrophic factor secretion. [GOC:TermGenie, GOC:yaf]
Any process that stops, prevents, or reduces the frequency, rate or extent of dopamine receptor protein 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 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]
The process in which a startle magnitude is reduced when the startling stimulus is preceded by a low-intensity prepulse. [GOC:dph, PMID:10341260]
Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell. [GOC:dph]
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 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 or increases the frequency, rate or extent of the directed movement of dopamine into a cell. [GOC:ai]
Any process that modulates the frequency, rate or extent of the directed movement of the catecholamine neurotransmitter dopamine into a cell. [GOC:ai]
Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.  Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. [GOC:ai]
The controlled release of arachidonic acid from a cell or a tissue. [GOC:ai]
The process in which the anatomical structures of branches in a nerve are generated and organized. This term refers to an anatomical structure (nerve) not a cell (neuron). [GOC:dgh, GOC:dph, GOC:jid]
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]
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 stops, prevents, or reduces the frequency, rate or extent of the innate immune response. [GOC:go_curators]
Any process in which the force of blood traveling through the circulatory system is decreased. [GOC:go_curators, GOC:mtg_cardio]
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. [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 morphine stimulus. Morphine is an opioid alkaloid, isolated from opium, with a complex ring structure. [CHEBI:17303, GOC:ef, GOC:jl]
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]
The chemical reactions and pathways involving dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline. [GOC:jl, ISBN:0198506732]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant. [CHEBI:27958, GOC:ef, GOC:jl]
Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size. [GOC:dph, GOC:go_curators, GOC:tb]
Any process that increases the amount of sodium excreted in urine over a unit of time. [GOC:mtg_25march11, GOC:yaf]
Any process that increases the amount of urine excreted from the body over a unit of time. [GOC:mtg_25march11, GOC:yaf]
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 histamine stimulus. Histamine, the biogenic amine 2-(1H-imidazol-4-yl)ethanamine, is involved in local immune responses as well as regulating physiological function in the gut and acting as a neurotransmitter. [CHEBI:18295, GOC:BHF, GOC:mah, GOC:vk]
Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours. [GOC:mah]
Any process that 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 modulates 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 modulates the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate). [GOC:mah]
Behavior in a fully developed and mature organism. [GOC:mah, ISBN:0877797099]
A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards. [ISBN:0198506732]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. [GOC:go_curators]
The progression of the adenohypophysis over time from its initial formation until its mature state. The adenohypophysis is the anterior part of the pituitary. It secretes a variety of hormones and its function is regulated by the hypothalamus. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. [GOC:go_curators, ISBN:0582227089]
Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue. [GOC:jid, ISBN:0582227089]
Learning by associating a stimulus (the cause) with a particular outcome (the effect). [ISBN:0582227089]
Any process that stops, prevents or reduces the rate or extent of cell proliferation. [GOC:go_curators]
Any process in which a protein is transported to, or maintained in, a specific location. [GOC:ai]
Behavior associated with the intake of food. [GOC:mah]
The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg. [GOC:jid, GOC:pr, ISBN:0198606907]
The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GOC:dph]
The 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 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/]
De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon. [GOC:dph, GOC:jid, GOC:pg, GOC:pr, ISBN:0198506732]
The process of communication from a neuron to another neuron across a synapse. [GOC:add, GOC:jl, MeSH:D009435]
The series of molecular signals generated as a consequence of a dopamine receptor binding to one of its physiological ligands. [GOC:mah]
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]
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 activates or increases the rate of neuroblast proliferation. [GOC:dph]
Any process that modulates 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]
Any process that modulates the frequency or rate of heart contraction. [GOC:dph, GOC:tb, PMID:10358008]
The regulation of blood pressure mediated by detection of stimuli and a neurological response. [GOC:mtg_cardio, ISBN:0721643949]
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]
An action or movement due to the application of a sudden unexpected stimulus. [GOC:dph]
A homeostatic process in which an organism modulates its internal body temperature. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
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]
Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease. [GOC:jl, ISBN:0198506732]
Combining with the neurotransmitter dopamine to initiate a change in cell activity. [IUPHAR_GPCR:1282]
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 directed movement of thiamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Thiamine is vitamin B1, a water soluble vitamin present in fresh vegetables and meats, especially liver. [GOC:ai]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:add, ISBN:0781735149]
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 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]
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]
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 membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The component of a 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]
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]
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 stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction. [GOC:bf]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein. [PMID:10037737, PMID:10068444, PMID:10940390]
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
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 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]
A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription. [GOC:ceb, GOC:signaling]
The process of introducing a phosphate group on to a protein. [GOC:hb]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [GOC:bf, GOC:ceb, ISBN:0198506732]
Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein. [EC:2.7.10.2]
Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. [EC:2.7.10]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
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 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 activates or increases the frequency, rate or extent of calcium-mediated signaling. [GOC:ai]
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 the chemical reactions and pathways resulting in the formation of granulocyte macrophage colony-stimulating factor. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-3. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of mast cell degranulation. [ISBN:0781735149]
A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region. [GOC:phg, PMID:12413516, PMID:15048725]
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 initiation of the activity of the inactive enzyme JUN kinase (JNK). [GOC:bf]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. [GOC:ef, ISBN:0198506732, ISBN:0781735149]
Any process that activates or increases the frequency, rate or extent of type I hypersensitivity, a type of inflammatory response. [GOC:add, ISBN:0781735149]
The initiation of the activity of the inactive enzyme MAP kinase (MAPK). [PMID:9561267]
Interacting selectively and non-covalently with an immunoglobulin of the IgE isotype. [GOC:add, ISBN:0781735149]
Combining with an immunoglobulin of the IgE isotype via the Fc region, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. [GOC:add, GOC:signaling, ISBN:0781735149]
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 extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II. [GOC:mah, GOC:txnOH]
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]
The modification of histone H3 by the addition of an acetyl group. [GOC:jl]
The modification of a histone by the addition of an acetyl group. [GOC:ai]
The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex. [GOC:mtg_cell_cycle]
Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule. [GOC:ai]
Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone. [EC:2.3.1.48]
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 modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
Stimulates the exchange of guanyl nucleotides associated with a GTPase 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 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 increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
Any process that modulates 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]
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]
A small (70-100 nm) cytoplasmic granule that contains a number of centrosomal proteins; centriolar satellites traffic toward microtubule minus ends and are enriched near the centrosome. [GOC:BHF, PMID:10579718, PMID:12403812]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides. [GOC:vw, http://en.wikipedia.org/wiki/Microtubule_organizing_center, ISBN:0815316194, PMID:17072892, PMID:17245416]
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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The 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 aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis. [GOC:tb, GOC:vw]
A process in which a protein is transported to, or maintained at, the centrosome. [GOC:ecd]
Any process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat6 protein. [GOC:jl, PMID:11426647]
Any process that stops, prevents, or reduces the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat4 protein. [GOC:jl, PMID:11426647]
Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation. [GOC:mah]
Any process that activates or increases the frequency, rate, or extent of interleukin-10 production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-12 production. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of prostaglandin. [GOC:mah]
The process of introducing a phosphate group to a tyrosine residue of a JAK1 (Janus Activated Kinase 1) protein, thereby activating it. [GOC:dph, GOC:tb, PMID:9135582]
The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis. [GOC:mah, ISBN:0815316194]
Interacting selectively and non-covalently with the interleukin-4 receptor. [GOC:ai]
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 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 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 endothelial cell apoptotic process. [GOC:BHF, GOC:mah, GOC:mtg_apoptosis]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:mah]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature. [GOC:BHF, GOC:dph]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons. [GOC:go_curators, GOC:mtg_apoptosis]
A 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 formation of a cross-link between peptide chains mediated by a chondroitin 4-sulfate glycosaminoglycan that originates from a typical O-glycosidic link to serine of one chain; the other chain is esterified, via the alpha-carbon of its C-terminal Asp, to C-6 of an internal N-acetylgalactosamine of the glycosaminoglycan chain. [PMID:1898736, RESID:AA0219]
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. [GOC:ai]
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules. [GOC:dph, GOC:pf, GOC:tb]
Any intracellular signal transduction in which the signal is passed on within the cell via nitric oxide (NO). Includes synthesis of nitric oxide, receptors/sensors for nitric oxide (such as soluble guanylyl cyclase/sGC) and downstream effectors that further transmit the signal within the cell. Nitric oxide transmits its downstream effects through either cyclic GMP (cGMP)-dependent or independent mechanisms. [GOC:jl, PMID:21549190]
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 inadequate blood supply. [GOC:hjd]
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]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with any glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues. [GOC:jl, ISBN:0198506732]
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]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
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]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
Any 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 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]
Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand. [GOC:mtg_apoptosis]
Any process that activates or increases the frequency, rate or extent of parathyroid hormone secretion. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of endothelial cell chemotaxis to fibroblast growth factor. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of mitotic cell cycle DNA replication. [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie, PMID:1234]
Any process that decreases the rate, frequency or extent of the appearance of a fibroblast growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. [GOC:BHF]
The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands resulting in an increase in the rate or frequency of a MAPKKK cascade. [GOC:dph, GOC:tb]
The chemical reactions and pathways involving vitamin D3, (3S,5Z,7E)-9,10-secocholesta-5,7,10(19)-trien-3-ol. [CHEBI:28940, GOC:BHF, GOC:mah]
Any process that modulates the rate, frequency, or extent of branching involved in salivary gland morphogenesis as a result of signals being generated by the mesenchyme and received and interpreted by the salivary gland epithelium. [GOC:dph, PMID:17336109]
The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung. [GOC:dph, GOC:mtg_lung]
The process in which the branching structure of the salivary gland is generated and organized. [GOC:dph]
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 activates or increases the frequency, rate or extent of cardiac muscle cell proliferation. [GOC:dph, GOC:rph]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. [GOC:ai]
The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types. [GOC:dph, GOC:jid]
The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons. [GOC:nln]
The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood. [GOC:jid]
A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of lateral mesoderm cell fate specification. [GOC:jid]
The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube. [GOC:dgh]
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 rate or extent of progression through the cell cycle. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of neuron differentiation. [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 activates or increases the frequency, rate or extent of MAP kinase activity. [GOC:dph, GOC:go_curators]
The process in which the anatomical structures of the middle ear are generated and organized. The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window). [GOC:jl, ISBN:0192801023]
The process in which the anatomical structures of the outer ear are generated and organized. The outer ear is the part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull. [GOC:jl, ISBN:0192801023]
The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively. [GOC:jl, ISBN:0192801023]
Any process that modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The series of molecular signals generated as a consequence of a fibroblast growth factor-type receptor binding to one of its physiological ligands, which contributes to the progression of the orbitofrontal cortex over time from its initial formation until its mature state. [GOC:yaf]
The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles). [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=midbrain]
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping. [GOC:bf, GOC:jl, ISBN:0395825172]
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. [GOC:jid, UBERON:0002048]
The proliferation of neuroblasts in the ventricular zone of the cerebral cortex. The neuronal progenitors of these cells will migrate radially. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The progression of the orbitofrontal cortex over time from its initial formation until its mature state. The orbitofrontal cortex is a cerebral cortex region located in the frontal lobe. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420]
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. [RESID:AA0039]
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
Any process that increases the rate of phospholipase C activity. [GOC:dph, GOC:tb]
Any process that 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 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 series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands. [GOC:ceb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
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 process in which the anatomical structures of the salivary gland are generated and organized. [GOC:jid]
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). [GOC:dph, GOC:jid, GOC:tb, UBERON:0000955]
The directed movement of phosphates into, out of or within a vacuole. [GOC:ai]
The process of introducing a phosphate group on to a protein. [GOC:hb]
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage. [GOC:dph]
The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells. [GOC:dph]
The interaction of two or more cells or tissues that causes them to change their fates and specify the development of an organ. [ISBN:0878932437]
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 the ureteric bud over time, from its formation to the mature structure. [GOC:go_curators]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The aggregation, arrangement and bonding together of two or more different receptor complexes that individually undergo combination with a hormone, neurotransmitter, drug or intracellular messenger to form a higher level receptor complex. The formation of the higher level complex initiates a change in cell function. [GOC:dox, GOC:pad, GOC:PARL, PMID:22035699, PMID:24157794]
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 a fibroblast growth factor. [PMID:9806903]
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 heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Combining with a fibroblast growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity. [GOC:mah]
Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate. [EC:2.7.10.1, GOC:mah]
Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. [EC:2.7.10]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. [MetaCyc:PROTEIN-KINASE-RXN]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The 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 cleavage of a carbon-oxygen bond by elimination of water. [EC:4.2.1]
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 multimeric protein complex that associates with the vacuolar membrane, late endosomal (multivesicular body) and lysosomal membranes. HOPS is a tethering complex involved in vesicle fusion. [PMID:10944212, PMID:23645161]
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]
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 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]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm. [GOC:jl]
Any process that modulates the frequency, rate or extent of assembly of the SNARE complex. The SNARE complex is 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. [GOC:rb]
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 substances from endosomes to lysosomes. [GOC:ai, ISBN:0716731363]
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]
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 initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis. [GOC:jid]
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 binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. [GOC:bf, GOC:mah, GOC:vw]
Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse. [ISBN:0198506732]
Interacting selectively and non-covalently with 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 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 activity of a GTPase. [GOC:jl, GOC:mah]
Any process that modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase. [GOC:mah]
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 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 stops, prevents or reduces the frequency, rate or extent of cellular senescence. [GOC:BHF]
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 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 activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with one of the p53 family of proteins. [GOC:hjd]
A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8. [PMID:10637607, PMID:17337012]
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 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]
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 methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative. [GOC:ai]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946]
Catalysis of the reaction: S-adenosyl-L-methionine + calmodulin L-lysine = S-adenosyl-L-homocysteine + calmodulin N6-methyl-L-lysine. [EC:2.1.1.60]
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]
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]
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 glucagon stimulus. [GOC:mah]
Any process in which the force of blood traveling through the circulatory system is increased. [GOC:go_curators, GOC:mtg_cardio]
Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell. [GOC:signaling]
Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. [GOC:dph, GOC:go_curators, GOC:tb]
The acquisition and processing of information and/or the storage and retrieval of this information over time. [GOC:jid, PMID:8938125]
Any process that increases the concentration of calcium ions in the cytosol. [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]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
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]
Combining with a peptide 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:dph, GOC:tb]
Combining with glucagon and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:mah, GOC:signaling, PMID:22438981]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. [GOC:go_curators, Wikipedia:Transmembrane_receptor]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. [GOC:go_curators]
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 contractile fiber of smooth muscle cells. [GOC:mah]
Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. [GOC:mah, GOC:pr, ISBN:0815316194]
A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments. [ISBN:0815316194]
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]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The process in which the population of cells that make up a mesenchyme undergo directed movement. [GOC:ascb_2009, GOC:dph, GOC:tb]
The process whose specific outcome is the progression of a glomerular mesangial cell in the kidney over time, from its formation to the mature structure. [GOC:mtg_kidney_jan10]
A process, occurring in the vascular tissue, whereby actin/myosin complex activity generates force through ATP hydrolysis resulting in a change in smooth muscle geometry. This process is always coupled to chemo-mechanical energy conversion. [GOC:mtg_muscle, MA:0002718]
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 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 modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. [GOC:dph, GOC:mtg_cardio, ISBN:0721643949]
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 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]
Any cytoplasm that is part of a axon. [GO_REF:0000064, GOC:TermGenie, PMID:18667152]
A membrane coat adaptor complex that links clathrin to a membrane. [GOC:mah]
The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
The directed movement of synaptic vesicle along axonal microtubules from the cell body to the presynapse. [GOC:jid, GOC:lmg]
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]
Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases. [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 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 external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that stops, prevents, or reduces the frequency, rate or extent of axon regeneration. [GOC:dgh, GOC:dph, GOC:jid, GOC:lm]
Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity. [GOC:bf]
The process whose specific outcome is the progression of the corpus callosum over time, from its formation to the mature structure. The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provide communication between the right and left cerebral hemispheres. [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
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 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 stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Interacting selectively and non-covalently with chondroitin sulfate, a glycosaminoglycan made up of two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc). [GOC:kmv, ISBN:0198506732]
Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The modification of a histone by addition of one or more methyl groups to a lysine residue. [GOC:mah, GOC:pr]
The process in which a methyl group is covalently attached to a molecule. [GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the reaction: S-adenosyl-L-methionine + histone 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]
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]
Any process that modulates the frequency, rate or extent of RNA polymerase II regulatory region sequence-specific DNA binding. [GO_REF:0000059, GOC:dph, GOC:krc, GOC:TermGenie, PMID:20026326]
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 the phosphorylation of peptidyl-serine. [GOC:mah]
The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone. [GOC:pr, GOC:tb]
Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3. [GOC:krc]
Interacting selectively and non-covalently with an androgen receptor. [GOC:ai]
Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group onto lysine at position 36 of the histone H3 protein. [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 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]
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 series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
The action of a molecule that contributes to the structural integrity of the lens of an eye. [GOC:mah]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. [GOC:go_curators]
Any process that modulates the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it. [ISBN:0198506732]
The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria. [GOC:pde, PMID:20559380, RESID:AA0040]
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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
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 iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group. [GOC:jl, ISBN:0198506732]
The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [CHEBI:30413, GOC:ai]
Interacting selectively and non-covalently with oxygen (O2). [GOC:jl]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
Enables the directed movement of oxygen into, out of or within a cell, or between cells. [GOC:ai]
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]
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 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 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, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113]
The process 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 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 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]
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]
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 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]
Any process that activates or increases the frequency, rate or extent of Arp2/3 complex-mediated actin nucleation. [PMID:21454476]
The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits. [GOC:hjd]
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. [GOC:dph, GOC:jl, GOC:mah]
A 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]
Any process that increases the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell. [GOC:dph, GOC:tb]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of the assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament. [GOC:mah]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. [GOC:mah]
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 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 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 process in which the anatomical structures of a mitochondrion are generated and organized. [GOC:mah]
Any process pertaining to the functions of the nervous and muscular systems of an organism. [GOC:ai]
The increase in size or mass of an entire organism, a part of an organism or a cell. [GOC:bf, GOC:ma]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. [GOC:go_curators]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
The part of a synapse that is part of the presynaptic cell. [GOC:dos]
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]
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 enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is 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:bf, GOC:BHF]
Any process that activates or increases the frequency, rate or extent of excitatory synapse assembly. [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:21670302]
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 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 transforming growth factor beta stimulus. [GOC:ecd, PMID:15451575]
The process in which anatomical structures of the uterus are generated and organized. [GOC:BHF, GOC:dph]
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]
The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin. [GOC:dgh, GOC:dph, PMID:11487378]
The 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 reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism. [GOC:dph, GOC:ebc, http://www.thefreedictionary.com/oviduct]
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]
Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury. [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]
Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. [GOC:ai, GOC:pr]
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]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). [GOC:ai, GOC:pr]
Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the origin and formation of neurons. [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]
The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. [GOC:jid, ISBN:0582227089]
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 commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. [ISBN:0716731185]
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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics. [GOC:jl, ISBN:0198506732]
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 series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of a cell in the epidermis that contributes to the migration of an epidermal cell along or through a wound gap to reestablish a continuous epidermis. [GOC:BHF]
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 effectors other than beta-catenin. [GOC:signaling]
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]
Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line. [GOC:bf, ISBN:0582227089]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. [GOC:mah]
Any process that modulates the rate, direction or extent of axon growth such that the correct diameter is attained and maintained. [GOC:dph, GOC:mah, GOC:tb]
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping. [GOC:bf, GOC:jl, ISBN:0395825172]
The process in which a relatively unspecialized cell acquires specialized features of a neuron. [GOC:mah]
The specification and formation of anisotropic intracellular organization or cell growth patterns. [GOC:mah]
The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The creation of greater cell numbers in the forebrain due to cell division of progenitor cells. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar granule cell. Differentiation includes the processes involved in commitment of a neuroblast to a granule cell fate. A granule cell is a glutamatergic interneuron found in the cerebellar cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15157725]
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 by which the number of skeletal muscle satellite cells in a skeletal muscle is maintained during muscle regeneration. There are at least three mechanisms by which this is achieved. Skeletal muscle satellite stem cell asymmetric division ensures satellite stem cell numbers are kept constant. Symmetric division of these cells amplifies the number of skeletal muscle satellite stem cells.  Some adult skeletal muscle myoblasts (descendants of activated satellite cells) can develop back into quiescent satellite cells, replenishing the overall pool of satellite cells. [GOC:dph, GOC:ef, GOC:mtg_muscle, GOC:tb, PMID:23303905]
The change of a skeletal muscle satellite cell from a mitotically quiescent to a mitotically active state following exposure to some activating factor  such as a cellular or soluble ligand. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage. [GOC:mtg_muscle, PMID:23303905]
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 regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism. [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
Any process in which a protein is transported to, or maintained in, a specific location such that it is distributed asymmetrically. [GOC:ma]
The 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 regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission. [CHEBI:25512, GOC:dph]
The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage. [GOC:dph]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. [ISBN:0878932453]
The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes. [ISBN:0878932437]
The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo. [GOC:dph, GOC:go_curators, GOC:sdb_2009, GOC:tb]
Interacts with receptors such that the proportion of receptors in the active form is increased. [GOC:ceb, ISBN:0198506732]
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]
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 non-F1 subunits of the mitochondrial hydrogen-transporting ATP synthase, including integral and peripheral mitochondrial inner membrane proteins. [GOC:mtg_sensu, PMID:10838056]
One of two stalks that connect the catalytic core of the hydrogen-transporting ATP synthase to the mitochondrial membrane-associated F0 proteins; is thought to prevent futile rotation of the catalytic core. [GOC:mtg_sensu, PMID:10838056]
The transport of an inorganic cation across a membrane and against an electrochemical gradient, using energy from ATP hydrolysis. [GOC:BHF]
The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis. [ISBN:0716731363]
Enables the transfer of hydrogen ions from one side of a membrane to the other. [GOC:ai]
Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ADP + H2O + phosphate + H+(in) = ATP + H+(out), by a rotational mechanism. [EC:3.6.3.14, TC:3.A.2.1.1]
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]
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 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 organic acid across a membrane. [GO_REF:0000069, GOC:TermGenie]
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]
Catalysis of the transfer of organic anions from one side of a membrane to the other, in a sodium independent manner. [GOC:go_curators]
Enables the transfer of urate from one side of the membrane to the other. Urate is the anion of uric acid, 2,6,8-trioxypurine, the end product of purine metabolism in certain mammals and the main excretory product in uricotelic animals. [GOC:ai]
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]
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 formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits. [GOC:go_curators]
Assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament. [GOC:mah]
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 monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Any process that stops, prevents, or reduces 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]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier. [GOC:dgh, GOC:mah]
A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state. [GOC:dph, GOC:jl]
The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia. [GOC:dgh, GOC:jid]
The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process aimed at the progression of a Schwann cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function. [GOC:dgh, GOC:ef]
The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others. [GOC:ef, ISBN:0878932585]
Locomotory behavior in a fully developed and mature organism. [GOC:ai]
A protein complex that possesses activity that prevents or downregulates transcription. [GOC:mah]
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 protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins. [PMID:11454195, PMID:16168358, PMID:17870225]
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]
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
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 bone development. [GO_REF:0000058, GOC:mr, GOC:TermGenie, PMID:22510437]
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 apoptotic process in a thymocyte, an immature T cell located in the thymus. [CL:0000893, GOC:add, GOC:mtg_apoptosis, ISBN:0781765196]
The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the kidney as it progresses from its formation to the mature state. [GOC:mtg_kidney_jan10]
The progession of the lateral semicircular canal from its initial formation to the mature structure. [GOC:dph, GOC:sdb_2009, GOC:tb]
The progession of the anterior semicircular canal from its initial formation to the mature structure. [GOC:dph, GOC:sdb_2009, GOC:tb]
The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed. [GOC:dph, GOC:sdb_2009, GOC:tb]
The series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened contributing to the dorsal/ventral pattern of the neural tube. [GOC:dph, GOC:sdb_2009, GOC:tb]
The regionalization process in which the mammary line is specified. The mammary line is a ridge of epidermal cells that will form the mammary placodes. [GOC:dph]
The process in which the sagittal suture is generated and organized. [GOC:dph, GOC:sl]
The process in which the lambdoid suture is generated and organized. [GOC:dph, GOC:sl]
The process in which the frontal suture is generated and organized. [GOC:dph, GOC:sl]
The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin. [GOC:dgh, GOC:dph, PMID:11487378]
The 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 biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. 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 inner ear over time, from its formation to the mature structure. [GOC:sr]
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]
The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. [GOC:vp, PMID:15139015]
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 developmental fate of a cell becomes restricted such that it will develop into a neuron. [GOC:dph]
The developmental process pertaining to the initial formation of an anatomical structure 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. 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. [GOC:dph, GOC:jid, GOC:tb]
The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. [GOC:jid, GOC:mtg_sensu]
The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. [GOC:jid, GOC:mtg_sensu]
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]
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 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 in which the anatomical structures of the digestive tract are generated and organized during embryonic development. The digestive tract is the anatomical structure through which food passes and is processed. [GOC:go_curators]
Any process that stops, prevents, or reduces 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 alpha-beta T cell differentiation. [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]
Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of osteoblast differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces 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 process of elimination of immature T cells in the thymus which react strongly with self-antigens. [ISBN:0781735149, PMID:12414722]
The process whose specific outcome is the progression of the tongue over time, from its formation to the mature structure. The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech. [GOC:jl, UBERON:0001723]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. [GOC:go_curators, GOC:mtg_sensu]
Any process that modulates the occurrence or rate 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]
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]
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 modulates the frequency, rate or extent of cell proliferation. [GOC:jl]
The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. [PMID:12526790]
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 in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus. [GOC:add, ISBN:0781735149]
Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation. [GOC:mah]
The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions). [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=forebrain]
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]
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping. [GOC:bf, GOC:jl, ISBN:0395825172]
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. [GOC:jid, UBERON:0002048]
The process in which a relatively unspecialized cell acquires specialized features of a melanocyte. [GOC:mah]
The multiplication or reproduction of lateral ganglionic eminence cells, resulting in the expansion of the cell population. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
The process in which neuroepithelial cells of the neural tube give rise to radial glial cells, specialized bipotential progenitors cells of the forebrain. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:16226447]
The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The radial migration of neuronal or glial precursor cells along radial glial cells during the development of the cerebral cortex. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
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 series of molecular signals initiated by binding of a ligand to the transmembrane receptor smoothened in a precursor cell in the spinal cord that contributes to the process of a precursor cell becoming capable of differentiating autonomously into a motor neuron in an environment that is neutral with respect to the developmental pathway. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15936325]
The series of molecular signals initiated by binding of a ligand to the transmembrane receptor smoothened in a precursor cell in the ventral spinal cord that contributes to the commitment of the precursor cell to an interneuron fate. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869]
The progression of the hippocampus over time from its initial formation until its mature state. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420, UBERON:0002421]
The process in which the anatomical structure of the optic nerve is generated and organized. The sensory optic nerve originates from the bipolar cells of the retina and conducts visual information to the brainstem. The optic nerve exits the back of the eye in the orbit, enters the optic canal, and enters the central nervous system at the optic chiasm (crossing) where the nerve fibers become the optic tract just prior to entering the hindbrain. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The process whose specific outcome is the progression of the subpallium over time, from its formation to the mature structure. The subpallium is the base region of the telencephalon. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The process whose specific outcome is the progression of the pallium over time, from its formation to the mature structure. The pallium is the roof region of the telencephalon. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695]
The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869]
The process that regulates the coordinated growth and differentiation that establishes the non-random dorsal-ventral spatial arrangement of the spinal cord. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
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]
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 regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end). [GOC:dph, GOC:go_curators, GOC:isa_complete]
The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism. [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
Any process that 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]
The process in which the anatomical structures of the hindgut are generated and organized. [GOC:jid]
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 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 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]
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]
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 cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the rate of neuroblast proliferation. [GOC:dph]
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]
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 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 metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine. [GOC:bf, ISBN:0192800752]
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 DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with the enzyme histone deacetylase. [GOC:jl]
Interacting selectively and non-covalently with the enzyme histone acetyltransferase. [GOC:bf]
Interacting selectively and non-covalently with the beta subunit of the catenin complex. [GOC:bf]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
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 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 structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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]
Any process that stops, prevents, or reduces the frequency, rate or extent of tooth mineralization, the deposition of calcium salts in tooth structures. [GOC:BHF, GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway. [GOC:mah]
The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue. [GOC:mah, PMID:22936354]
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 stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
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 calcium ions (Ca2+). [GOC:ai]
Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
A protein complex consisting of cyclin E2 and cyclin-dependent kinase 2 (CDK2). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner. [GOC:so, PMID:15935619, PR:000026746]
A protein complex consisting of cyclin E1 and cyclin-dependent kinase 2 (CDK2). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner. [GOC:so, PMID:15935619, PR:000026745]
A protein complex consisting of cyclin A2 and cyclin-dependent kinase 2 (CDK2). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner. [GOC:so, PMID:15935619]
A protein complex consisting of cyclin A1 and cyclin-dependent kinase 2 (CDK2). Cyclins are characterized by periodicity in protein abundance throughout the cell cycle. Cyclin-dependent kinases represent a family of serine/threonine protein kinases that become active upon binding to a cyclin regulatory partner. [GOC:so, PMID:15935619]
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 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 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]
The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males. [GOC:mah, GOC:mr, https://en.wikipedia.org/wiki/XY_sex-determination_system, ISBN:0582227089, PMID:20622855]
The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males. [GOC:mah, GOC:mr, https://en.wikipedia.org/wiki/XY_sex-determination_system, ISBN:0582227089, PMID:20622855]
A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure. [GOC:elh]
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
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, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. [GOC:dph, GOC:tb]
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 initiation of DNA-dependent DNA replication. [GOC:mah]
The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine. [RESID:AA0037]
The modification of histones by addition of phosphate groups. [GOC:ai]
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that modulates the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle. [GOC:mtg_cell_cycle, PMID:17329565]
Any process that 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]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
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 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 cell cycle process in which a daughter centriole is formed perpendicular to an existing centriole. An immature centriole contains a ninefold radially symmetric array of single microtubules; mature centrioles consist of a radial array of nine microtubule triplets, doublets, or singlets depending upon the species and cell type. Duplicated centrioles also become the ciliary basal body in cells that form cilia during G0. [GOC:cilia, GOC:kmv, ISBN:0815316194, PMID:9889124]
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 process of introducing a phosphate group on to a protein. [GOC:hb]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated. [GOC:mtg_cell_cycle]
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK). [GOC:pr]
Catalysis of the transfer of a phosphate group to a histone. Histones are any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. [GOC:bf]
Interacting selectively and non-covalently with cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis. [GOC:ai]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK). [GOC:pr, GOC:rn, PMID:7877684, PMID:9841670]
Catalysis of the 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 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 activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
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]
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 removal of phosphoric residues from peptidyl-O-phospho-L-serine to form peptidyl-serine. [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 morphine stimulus. Morphine is an opioid alkaloid, isolated from opium, with a complex ring structure. [CHEBI:17303, GOC:ef, GOC:jl]
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 process of removing one or more phosphoric residues from a protein. [GOC:hb]
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. [GOC:mah, ISBN:0815316194, Reactome:69278]
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
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 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 of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. [ISBN:0879693568]
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [GOC:mah, ISBN:0198547684, PMID:16959967]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules. [GOC:clt]
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 vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. [GOC:bf, GOC:cilia, ISBN:0198547684]
Any multimeric complex connected to a microtubule. [GOC:jl]
Any process that stops, prevents or reduces the frequency, rate or extent of non-motile cilium assembly. [GO_REF:0000058, GOC:cilia, GOC:kmv, GOC:TermGenie, PMID:23807208]
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. [GOC:di, GOC:go_curators, GOC:pr]
Any process that set the alignment of spindle relative to other cellular structures. [GOC:ai]
The movement of one microtubule along another microtubule. [PMID:14557818, PMID:14614826]
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]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle. [GOC:go_curators, GOC:mah]
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 microtubules, filaments composed of tubulin monomers. [GOC:krc]
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]
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]
A distinct compartment at the tip of a stereocilium, distal to the site of attachment to the apical cell surface. It consists of a dense matrix bridging the barbed ends of the stereocilium actin filaments with the overlying plasma membrane. [GOC:ecd, PMID:17021180]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
Any process that modulates the frequency, rate or extent of calcium ion transmembrane transport. [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:24125847]
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 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]
A reflex process in which a response to an angular or linear acceleration stimulus begins with an afferent nerve impulse from a receptor in the inner ear and ends with the compensatory action of eye muscles. Signaling never reaches a level of consciousness. [PMID:11784757]
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]
Enables the transmembrane transfer of an ion by a channel that opens in response to a mechanical stress. [GOC:mtg_transport, ISBN:0815340729]
Enables the transmembrane transfer of a calcium 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, GOC:tb, ISBN:0815340729]
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]
An assembly of six molecules of connexin, made in the Golgi apparatus and subsequently transported to the plasma membrane, where docking of two connexons on apposed plasma membranes across the extracellular space forms a gap junction. [PMID:11146276]
A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins. [GOC:mah, GOC:mtg_muscle, http://en.wikipedia.org/wiki/Gap_junction, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_g.html, ISBN:0815332181, PMID:22366062]
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 mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. [GOC:mah]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. [GOC:ai, GOC:dos]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. [GOC:go_curators, ISBN:0582227089]
The aggregation, arrangement and bonding together of a set of components to form a synapse.  This process ends when the synapse is mature (functional). [GOC:mah]
The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. [GOC:ems, GOC:mtg_sensu]
A wide pore channel activity that enables a direct cytoplasmic connection from one cell to an adjacent cell. The gap junction can pass large solutes as well as electrical signals between cells. Gap junctions consist of two gap junction hemi-channels, or connexons, one contributed by each membrane through which the gap junction passes. [GOC:dgh, 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]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription. [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR]
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. [GOC:go_curators, Wikipedia:Transmembrane_receptor]
The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. [GOC:dos, GOC:mah]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature. [GOC:BHF, GOC:dph]
Any process involved in the maintenance of an internal steady state of glucose within an organism or cell. [GOC:go_curators]
A series of molecular signals initiated by the binding of adiponectin 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:20536390]
A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription.  The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576). [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor]
Combining with an adipokinetic hormone to initiate a change in cell activity. Adipokinetic hormones (AKHs) are peptide hormones that are involved in the mobilization of sugar and lipids from the insect fat body during energy-requiring activities such as flight and locomotion. They also contribute to hemolymph sugar homeostasis. [GOC:sart, PMID:11904407]
Interacting selectively and non-covalently with adiponectin, a protein hormone produced by adipose tissue that modulates a number of metabolic processes, including glucose regulation and fatty acid catabolism. [GOC:BHF, GOC:rl, PMID:15210937]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone. [CHEBI:24621, GOC:jl]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
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:mtg_apoptosis, PMID:21760595]
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 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]
Reactions triggered in response to the presence of a virus that act to protect the cell or organism. [GOC:ai]
The chemical reactions and pathways resulting in the formation of any type I interferon. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. [GOC:add]
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 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 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 initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system. [GOC:mah, GOC:signaling, PMID:15379975]
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 process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Any process that 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 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 a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to 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]
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 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]
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 transfer of a substance from one side of a membrane to the other. [GOC:mtg_transport, ISBN:0815340729]
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]
Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment. [GOC:nln, GOC:sl, PMID:1754851, PMID:21551097]
An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed. [GOC:mh]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential. [GOC:mah]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A process in which a potassium ion is transported from one side of a membrane to the other. [GOC:mah]
The process in which membrane potential increases with respect to its steady-state potential, usually from negative potential to a more negative potential. For example, during the repolarization phase of an action potential the membrane potential often becomes more negative or hyperpolarized before returning to the steady-state resting potential. [GOC:dph]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. [GOC:mah]
The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states. [GOC:krc]
Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
Enables the transmembrane transfer of a potassium ion by a 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]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
The component of a 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 component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface. [GOC:dos, GOC:tb]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus. [GOC:mtg_sensu, ISBN:0198547684]
Interacting selectively and non-covalently with a heparan sulfate proteoglycan, any proteoglycan containing heparan sulfate as the glycosaminoglycan carbohydrate unit. [ISBN:0198506732]
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 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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The directed movement of synaptic vesicle along axonal microtubules from the cell body to the presynapse. [GOC:jid, GOC:lmg]
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 cytoplasm that is part of a axon. [GO_REF:0000064, GOC:TermGenie, PMID:18667152]
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]
Any process that activates or increases the frequency, rate or extent of mesenchymal stem cell differentiation. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of mesenchymal stem cell proliferation. [GOC:pm, GOC:TermGenie, PMID:18672106]
The release of transforming growth factor beta (TGF-beta) from its latent state. TGF-beta is secreted as part of a large latent complex (LLC) that is targeted to the extracellular matrix. Release of TGFbeta from its latent state is required for TGFbeta to bind to its receptors, and can occur by a variety of mechanisms. [GOC:bf, GOC:sl, PMID:12482908, PMID:9170210]
Interacting selectively and non-covalently with TGF-beta, transforming growth factor beta, a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types. [ISBN:0198506732]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The orderly movement of a skeletal muscle satellite cell from one site to another. Migration of these cells is a key step in the process of growth and repair of skeletal muscle cells. [GO_REF:0000091, GOC:mr, GOC:TermGenie, PMID:17996437, PMID:19609936]
The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface. [GOC:jl]
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]
A protein complex which is capable of inward rectifier potassium channel activity. [GO_REF:0000088, GOC:bhm, GOC:TermGenie, PMID:16834334]
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]
An ion channel complex through which potassium ions pass. [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]
A vacuole to which materials ingested by endocytosis are delivered. [ISBN:0198506732, PMID:19696797]
A process in which a potassium ion is transported from one side of a membrane to the other. [GOC:mah]
Any process that modulates the establishment or extent of a resting potential, the electrical charge across the plasma membrane, with the interior of the cell negative with respect to the exterior. The resting potential is the membrane potential of a cell that is not stimulated to be depolarized or hyperpolarized. [GOC:dph, GOC:ef, ISBN:0195088433]
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:vw]
The 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 transport of a potassium ion across a membrane via a narrow pore channel that is open even in an unstimulated or 'resting' state. [GOC:mtg_transport, ISBN:0815340729]
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 facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
Enables the transmembrane transfer of a potassium ion by 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]
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 targeting to mitochondrion. [GO_REF:0000058, GOC:pad, GOC:PARL, GOC:TermGenie, PMID:24270810]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. [GOC:dph, GOC:jl, GOC:mah]
A 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]
Any process that modulates the surface configuration of a cell. [GOC:dph, 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]
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]
The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated. [GOC:mtg_cell_cycle]
Interacting selectively and non-covalently with 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]
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 lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process. [GOC:BHF, GOC:expert_pt, GOC:mah, GOC:pde, GOC:rl]
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]
An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals. [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 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]
The directed movement of a motile cell or organism towards a higher concentration of a chemical. [GOC:ai, GOC:bf, GOC:isa_complete]
Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal. [GOC:go_curators, 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 series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. [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]
Combining with a pheromone to initiate a change in cell activity. A pheromone is a substance used in olfactory communication between organisms of the same species eliciting a change in sexual or social behavior. [CHEBI:26013, GOC:hjd, ISBN:0198506732]
A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck. [ISBN:0198504888, NIF_Subcellular:sao1145756102]
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 portion of the plasma membrane surrounding a filopodium. [GOC:mah]
Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft. [GOC:mah, GOC:pr, ISBN:0815316194]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The process of directing proteins towards the plasma membrane; usually uses signals contained within the protein. [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 electrical stimulus. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of dopamine receptor protein 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 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 activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone. [GOC:ai, GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces 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 modulates the surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
Any process in which a protein is transported to, or maintained in, a specific location. [GOC:ai]
Any process that stops, prevents, or reduces the frequency, rate or extent of adenylate cyclase activity. [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 cytoskeletal structures. [GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with a D3 dopamine receptor. [GOC:mah, GOC:nln]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
Interacting selectively and non-covalently with calcium ions (Ca2+). [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 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]
An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. [ISBN:0198506732]
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 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 lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity. [GOC:obol]
Any process that modulates the activity of an enzyme. [GOC:ai, GOC:ebc, GOC:vw]
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]
Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP. [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]
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 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]
Any process that modulates the frequency, rate or extent of superoxide dismutase activity. [GOC:TermGenie]
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. [GOC:jl]
The process in which the anatomical structures of the corpus callosum are generated and organized. The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provides communications between the right and left cerebral hemispheres. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. [GOC:go_curators]
The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. [GOC:bf, GOC:jid, ISBN:0582227089]
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]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
The action of a molecule that contributes to the structural integrity of the ribosome. [GOC:mah]
A macromolecular complex containing both protein and RNA molecules. [GOC:vesicles]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
The portion of the cell soma (neuronal cell body) that excludes the nucleus. [GOC:jl]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A prolongation or process extending from a cell, e.g. a flagellum or axon. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A ribonucleoprotein granule located in the cytoplasm. [GOC:bf, GOC:PARL, PMID:15121898]
A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus. [PMID:16434402, PMID:17023415]
An intracellular macromolecular complex containing both protein and RNA molecules. [GOC:krc, GOC:vesicles]
The migrating motile tip of a growing nerve cell axon or dendrite. [ISBN:0815316194]
Specific locations and structures in the virus infected cell involved in replicating the viral genome. [ISBN:0781718325]
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 multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. [ISBN:0198506732, NIF_Subcellular:sao1038025871]
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]
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 response to DNA damage stimulus. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA. [GOC:dph]
Any process that activates or increases the frequency, rate or extent of mRNA binding. [GOC:rb, GOC:TermGenie, PMID:22890846]
Any process that activates or increases the frequency, rate or extent of intracellular transport of viral material. [GOC:bf, GOC:jl, GOC:TermGenie]
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 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 from a virus. [GOC:dos]
Any process that modulates the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. [GOC:dph]
Any process that modulates the rate, frequency, or extent of the 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: mRNA cleavage or translational repression. [GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone. [GOC:ai, GOC:dph, GOC:tb]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:dph, GOC:go_curators, GOC:tb]
A process in which a host organism modulates the frequency, rate or extent of viral RNA genome replication. [GOC:jl]
Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
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 that activates or increases the frequency, rate or extent of receptor internalization. [GOC:hjd]
Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs. [GOC:krc]
Interacting selectively and non-covalently with messenger RNA (mRNA) of a specific nucleotide composition or a specific sequence motif. [PMID:11886857]
Interacting selectively and non-covalently with the 5' untranslated region of an mRNA molecule. [GOC:jid]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
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 any part of a ribosome. [GOC:go_curators]
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 a stem-loop in an RNA molecule. 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 a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes. [PMID:15066283]
Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme. [PMID:15066275, PMID:15066283]
Interacting selectively and non-covalently with a histone protein in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. [GOC:bf, PMID:14585615]
Interacting selectively and non-covalently with a sequence of guanine residues in an RNA molecule. [GOC:mah]
Facilitates the base-pairing of complementary single-stranded RNA. [GOC:mah]
Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation. [GOC:mah]
Antagonizes ribosome-mediated translation of mRNA into a polypeptide. [GOC:ai, GOC:clt]
Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule. [GOC:mah]
Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule. [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 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]
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 the regulated release of cytokines from a cell. [GOC:ai]
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. [GOC:jl]
A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin G (IgG) to an Fc-gamma receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region. [GOC:phg, PMID:11244038]
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. [GOC:add, ISBN:0781735149]
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]
Combining with an extracellular or intracellular messenger to initiate a change in cell activity. [GOC:ceb, ISBN:0198506732]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered. [GOC:mah, GOC:mtg_apoptosis]
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]
Interacting selectively and non-covalently with one of the p53 family of proteins. [GOC:hjd]
A protein complex formed by the association of sterol regulatory element binding protein (SREBP), SREBP-cleavage-activating protein (SCAP), and an Insig protein (Insig-1 or Insig-2) in the ER membrane. [PMID:12923525]
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 process in which any suture between cranial bones is generated and organized. [GOC:dph, GOC:pr, GOC:sl]
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 stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids. [GOC:go_curators]
The process in which the anatomical structures of the middle ear are generated and organized. The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window). [GOC:jl, ISBN:0192801023]
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]
A series of molecular signals from the endoplasmic reticulum to the nucleus generated as a consequence of decreased levels of one or more sterols (and in some yeast, changes in oxygen levels) and which proceeds through activation of a sterol response element binding transcription factor (SREBP) to result in up-regulation of target gene transcription. [GOC:bf, GOC:mah, GOC:signaling, GOC:vw, PMID:12923525, PMID:22017871]
The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. [GOC:go_curators]
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. [GOC:BHF, GOC:tb]
The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. [ISBN:0198506732]
The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. [ISBN:0198547684]
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 deprivation of sterols. Sterols are a group of steroids characterized by the presence of one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. [GOC:bf, ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. [GOC:ai]
The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins. [ISBN:0198506732]
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
The 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 substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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 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 immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
Any process that 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 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]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. [ISBN:0198506732]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone. [GOC:ai, GOC:pr]
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 histones by removal of acetyl groups. [GOC:ai]
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. [GOC:mah, ISBN:0815316194, Reactome:69278]
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 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 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 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 transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH]
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 heterodimer associated with precursors of the eukaryotic small ribosomal subunit, including the 90S preribosome; involved in small subunit biogenesis. [PMID:12446671]
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 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]
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 an RNA molecule or a portion thereof. [GOC:mah]
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]
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 ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments. [GOC:clt]
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]
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 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]
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]
Muscle contraction of cardiac muscle tissue. [GOC:dph]
The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure. [GOC:dph, GOC:jid, GOC:lm]
The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP, as it occurs in the mitochondrial inner membrane or chloroplast thylakoid membrane. [GOC:mtg_sensu, ISBN:0716731363]
The assembly of cristae, the inwards folds of the inner mitochondrial membrane. [GOC:jl, ISBN:0198506732]
Remodeling the acyl chains of premature (de novo synthesized) cardiolipin (1,3-bis(3-phosphatidyl)glycerol), through sequential deacylation and re-acylation reactions, to generate mature cardiolipin containing high-levels of unsaturated fatty acids. [GOC:bf, GOC:rb, PMID:19244244]
The aggregation, arrangement and bonding together of a set of components to form mitochondrial respiratory chain complex I. [GOC:rph]
The chemical reactions and pathways resulting in the formation of cardiolipin, 1,3-bis(3-phosphatidyl)glycerol. [CHEBI:28494, GOC:mah]
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. [GOC:dgh, ISBN:0198506732]
The 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 developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers. [GOC:mtg_muscle]
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. [GOC:jid, UBERON:0000948]
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the mitochondrial inner membrane. [GOC:ai, GOC:dph, GOC:jl, 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 chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester. [ISBN:0198506732]
Catalysis of the reaction: 1-acyl-sn-glycero-3-phosphocholine + acyl-CoA = phosphatidylcholine + CoA. [EC:2.3.1.23, MetaCyc:2.3.1.23-RXN]
Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). [GOC:jl, ISBN:0198506732]
Catalysis of the transfer of an acyl group to an oxygen atom on the acceptor molecule. [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 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]
A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae). [GOC:bhm, GOC:mah, GOC:vw]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity. [GOC:BHF, GOC:mah]
Any process that activates or increases the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782]
Any process that initiates the activity of an inactive protein kinase. [GOC:mah]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. [GOC:go_curators]
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 stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of glycolysis. [GOC:go_curators]
The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. [ISBN:0198506732]
Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate. [GOC:jl]
Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
Interacting selectively and non-covalently with a 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 phosphorylase kinase. [EC:2.7.11.19]
Modulation of the activity of the enzyme cAMP-dependent protein kinase. [GOC:ai]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Stops, prevents or reduces the activity of a cAMP-dependent protein kinase. [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]
The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states. [GOC:hjd, GOC:mah, GOC:pde]
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 reaction: H2CO3 = CO2 + H2O. [EC:4.2.1.1]
Any process involved in the maintenance of an internal steady state of chloride ions within an organism or cell. [GOC:jid, GOC:mah]
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]
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 synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III 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]
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]
A protein complex that recognizes the proximal sequence element of RNA polymerase II and III snRNA promoters. [PMID:7715707, PMID:9003788]
The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter. [GOC:jl, ISBN:0321000382]
The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter. [GOC:jl, ISBN:0321000382]
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 synthesis of small nuclear RNA (snRNA) from a DNA template. [GOC:jl, ISBN:0321000382]
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 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]
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 function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II. [GOC:txnOH, PMID:16858867]
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 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]
Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway. [GOC:dph, GOC:go_curators, 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 by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered. [GOC:go_curators, GOC:mtg_apoptosis]
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 DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with the enzyme histone deacetylase. [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]
A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection. [GOC:ma, PMID:10944585]
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 retinoic acid receptor signaling pathway activity. [GOC:dgh]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
A series of molecular signals mediated by a steroid hormone binding to a receptor. [PMID:12606724]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Any process that 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 DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with the enzyme histone deacetylase. [GOC:jl]
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]
Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function. [GOC:signaling, PMID:14708019]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
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 nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex is known to contain TERF1, TERF2, POT1, RAP1, TINF2 and ACD in mammalian cells, and Pot1, Tpz1, Rap1, Rif1, Rif2 and Taz1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1, which acts as an effector molecule along with Ccq1. [GOC:expert_mf, GOC:mah, GOC:vw, PMID:18828880]
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. [GOC:ma, PMID:10330182]
A chromocenter adjacent to the nucleolus. [PMID:15805479]
The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome. [GOC:elh]
The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome. [GOC:BHF, GOC:mah]
Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). [GOC:ai]
Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. [GOC:ai]
Any process in which a protein is transported to, or maintained at, a specific location on a chromosome. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of telomeric repeats by telomerase. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA. [GOC:mah]
A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a telomere at a non-telomeric double-stranded DNA end. A telomere is a terminal region of a linear chromosome that includes telomeric DNA repeats and associated proteins. [GOC:mah, GOC:ns, PMID:11902675, PMID:8622671]
Any process that decreases the frequency, rate or extent of protein ADP-ribosylation. Protein ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids. [GOC:BHF, GOC:dph, GOC:tb]
Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and lengthening the telomeric DNA. [GOC:dph, GOC:tb]
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]
Stops, prevents or reduces the activity of a telomerase. Telomerase catalyzes the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence. [GOC:dph, GOC:krc, GOC:tb]
The removal of one or more ubiquitin groups from a protein. [GOC:ai]
The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein. [GOC:go_curators]
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]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE]
A protein complex that forms a subcomplex of the 90S preribosome and can interact directly with the 5' External Transcribed Spacer (ETS) of the full length pre-rRNA transcript. In S. cerevisiae, it sediments at 25-30 S and is composed of Pwp2p, Dip2p, Utp21p, Utp13p, Utp18p, and Utp6p. [GOC:krc, PMID:15231838]
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 conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. [GOC: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 small nucleolar RNA. [GOC:mah]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. [PMID:11532962, PMID:11743026]
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]
Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits. [PMID:11884619]
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 minimal catalytic core of telomerase is a ribonucleoprotein complex composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. [GOC:BHF-UCL, PMID:11884619, PMID:1808260]
Any process that stops, prevents or reduces the frequency, rate or extent of telomere capping. [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:23959892]
The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. [GOC:dph, GOC:tb]
The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis. [GOC:dph, GOC:tb]
Any process that modulates the propensity of RNA molecules to degradation. Includes processes that both stabilize and destabilize RNAs. [GOC:jl]
The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase. [GOC:elh]
The directed movement of mRNA from the nucleus to the cytoplasm. [GOC:ma]
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]
The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins. [GOC:krc, GOC:ma, PMID:10025395]
Interacting selectively and non-covalently with a DNA polymerase. [GOC:BHF, GOC:mah]
Interacting selectively and non-covalently with the telomerase RNA template. [GOC:krc, PMID:16884717]
Interacting selectively and non-covalently with any complex of RNA and protein. [GOC:bf, GOC:go_curators, GOC:vk]
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]
Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. [GOC:mah, ISBN:0198547684]
Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks. [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 portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. [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]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The external part of the cell wall and/or plasma membrane. [GOC:jl, GOC:mtg_sensu, GOC:sm]
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals. [GOC:dgh, GOC:hb, GOC:mah]
The 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 lipid bilayer surrounding the endoplasmic reticulum. [GOC:mah]
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 thyroid hormone generation. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of hepatocyte proliferation. [GOC:BHF, GOC:mah]
The reflex process in which the arrectores pilorum (hair follicle) muscles contract and cause the hair to stand erect. [GOC:BHF, http://en.wikipedia.org/wiki/Pilomotor_reflex, PMID:21335239]
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 thyroid hormone stimulus. [GOC:sjw, PMID:9916872]
The process in which the cochlea is generated and organized. [GOC:dph, GOC:tb]
A process in which a potassium ion is transported from one side of a membrane to the other. [GOC:mah]
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]
Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. [GOC:ai]
Any process in which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA. [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 controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion. [GOC:sart, PMID:17301221]
Any process that activates or increases the frequency, rate, extent or direction of cell growth. [GOC:go_curators]
Any process that increases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin. [GOC:BHF, GOC:dph, GOC:tb]
Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. [GOC:BHF, GOC:dph, GOC:tb]
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 surface configuration of a cell. [GOC:dph, GOC:go_curators, GOC:tb]
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 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 peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#EXOPEPTIDASE, ISBN:0716720094]
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]
Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient. [GOC:dph, GOC:mtg_transport]
Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
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]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094]
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 multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling. [GOC:bf, PMID:10412979]
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]
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]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein. [GOC:jl, PMID:11265250]
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 phosphorylated protein. [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 histone protein in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. [GOC:bf, PMID:14585615]
Interacting selectively and non-covalently with the small ubiquitin-like protein SUMO. [GOC:mah]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
Interacting selectively and non-covalently with single-stranded RNA. [GOC:jl]
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. [GOC:jl, ISBN:0198506732, PMID:20404130]
Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA; comprises subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). [ISBN:0716720094]
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 resulting in the formation of acetyl-CoA from pyruvate. [GOC:dph, GOC:go_curators, GOC:tb]
Catalysis of the reaction: pyruvate + CoA + NAD+ = acetyl-CoA + CO2 + NADH. [GOC:mah, ISBN:0201090910]
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]
An ion channel complex through which chloride ions pass. [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 chloride across a membrane. [GOC:TermGenie, GOC:vw]
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 facilitated diffusion of a chloride (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 end of a filopodium distal to the body of the cell. [GOC:mah]
The portion of the plasma membrane surrounding a filopodium. [GOC:mah]
The lipid bilayer surrounding the smooth endoplasmic reticulum. [GOC:mah]
The assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone. [GOC:dph, GOC:mah, GOC:tb, PMID:16337369, PMID:18464790]
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 attachment of a cell to the underlying substrate via adhesion molecules. [GOC:mah, GOC:pf]
The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism. [GOC:hb]
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]
Enables the transmembrane transfer of a chloride ion by a volume-sensitive channel. A volume-sensitive channel is a channel that responds to changes in the volume of a cell. [GOC:mah]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon. [GOC:pad, GOC:PARL]
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]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
An electron dense network of proteins within and adjacent to the postsynaptic membrane in asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. [GOC:BHF, GOC:dos, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density]
The lipid bilayer surrounding an endosome. [GOC:mah]
A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways. [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797]
A 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 brain-derived neurotrophic factor stimulus. [PMID:21958434]
Any process that modulates the frequency, rate or extent of excitatory postsynaptic potential (EPSP). EPSP is 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:dos]
Long distance growth of a single dendrite involved in cellular development. [GOC:BHF, GOC:rl]
A process that results in the assembly, arrangement of constituent parts, or disassembly of a postsynaptic density, a region that lies adjacent to the cytoplasmic face of the postsynaptic membrane at excitatory synapse. [GOC:BHF, GOC:sjp, PMID:21525273]
Any process that activates or increases the frequency, rate or extent of the neurotrophin TRK receptor signaling pathway. [GOC:ai]
The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:mah]
The process whose specific outcome is the progression of the dentate gyrus over time, from its formation to the mature structure. The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343]
The directed movement of organelles or molecules along microtubules from the cell periphery toward the cell body in nerve cell axons. [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]
Any cytoplasm that is part of a axon. [GO_REF:0000064, GOC:TermGenie, PMID:18667152]
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 that possesses activity that prevents or downregulates transcription. [GOC:mah]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. [GOC:dph, GOC:tb]
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]
The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang that results in the repair of a double strand break via single-strand annealing. [GOC:dph, GOC:tb]
A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts). [PMID:10197977]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
The hatching of the cellular blastocyst from the zona pellucida. [GOC:dph, ISBN:0124020607, ISBN:0198542771]
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]
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated. [GOC:mtg_cell_cycle]
Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. [GOC:mah, ISBN:0198547684]
Interacting selectively and non-covalently with damaged DNA. [GOC:jl]
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]
Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks. [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]
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 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 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 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]
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 process that stops, prevents or reduces the frequency, rate or extent of lipid binding. [GOC:pm, GOC:TermGenie]
The directed movement of a protein to a specific location in a peroxisome. [GOC:mah]
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]
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 involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation. [GOC:ai]
The targeting of proteins into the peroxisomal membrane. The process is not well understood, but both signals and mechanism differ from those involved in peroxisomal matrix protein import. [ISBN:0716731363, PMID:11687502]
The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments. [GOC:mah, PMID:11687502, PMID:14754507]
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]
The process of directing proteins towards the peroxisome, usually using signals contained within the protein. [GOC:ai]
Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP. [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 class I peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane in a PEX19-dependent manner. [GOC:pm, PMID:14709540, PMID:17020786]
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 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]
Interacting selectively and non-covalently with iron (Fe) ions. [GOC:ai]
An endoplasmic reticulum part at which COPII-coated vesicles are produced. [NIF_Subcellular:sao124393998, PMID:15623529, PMID:16957052]
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 continuous network of membranes encompassing the nuclear outer membrane and the endoplasmic reticulum membrane. [GOC:bf, GOC:jl, GOC:mah, GOC:mcc, GOC:pr, GOC:vw]
A vesicle that mediates transport from the endoplasmic reticulum to the Golgi complex; bears a coat formed of the COPII coat complex proteins; such vesicles found associated with endoplasmic reticulum (ER) membranes at steady state, and are involved in ER to Golgi (anterograde) vesicle transport. [GOC:ascb_2009, GOC:dph, GOC:mah, GOC:tb, PMID:11252894]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Any process that modulates the rate, frequency, or extent of ER to Golgi vesicle-mediated transport, 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:dph, GOC:tb]
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 membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol 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]
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 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]
Enables the transmembrane transfer of an ion by a channel that opens in response to a mechanical stress. [GOC:mtg_transport, ISBN:0815340729]
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]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. [GOC:mah]
The series of events by which a mechanical stimulus is received and converted into a molecular signal. [GOC:ai, GOC:dos]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
Enables the energy-independent passage of cations across a lipid bilayer down a concentration gradient. [GOC:def, GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
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]
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions. [PMID:16645198, PMID:20044567]
A 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]
A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis.  Caveolae may be pinched off to form free vesicles within the cytoplasm. [GOC:mah, ISBN:0721662544, PMID:16645198]
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 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 process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit. [GOC:mah, GOC:txnOH, PMID:10684922]
Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription. [GOC:mah, GOC:txnOH]
Interacting selectively and non-covalently with an unprocessed ribosomal RNA transcript. [GOC:jl]
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 process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
A 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 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 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 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]
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 network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination. [GOC:vw, ISBN:0815316194]
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. [ISBN:0198506732]
A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center. [NIF_Subcellular:nlx_subcell_20090702, PMID:11964142, PMID:2557062]
The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH. [GOC:imk]
The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH. [GOC:jl, ISBN:0618254153]
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. [GOC:curators, ISBN:0198547684]
Catalysis of the reaction: ATP + nicotinate ribonucleotide = diphosphate + deamido-NAD+. [EC:2.7.7.18]
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: ATP + nicotinamide nucleotide = diphosphate + NAD+. [EC:2.7.7.1]
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]
Distinctive, unmyelinated axons produced by granule cells. [NIF_Subcellular:nlx_subcell_20090601, PMID:17765709]
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. [GOC:go_curators]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
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]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway. [GOC:mtg_apoptosis]
Any process that modulates the frequency, rate or extent of signal transduction mediated by the JNK cascade. [GOC:bf]
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. [GOC:ai, GOC:mah, ISBN:08789310662000]
Any process that activates or increases the frequency, rate or extent of signal transduction. [GOC:sm]
The process of introducing a phosphate group into a JUN protein. [GOC:jl]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [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]
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]
The binding activity of a molecule that functions as a physical support for the assembly of a multiprotein mitogen-activated protein kinase (MAPK) complex. Binds multiple kinases of the MAPKKK cascade, and also upstream signaling proteins, permitting those molecules to function in a coordinated way. Bringing together multiple enzymes and their substrates enables the signal to be transduced quickly and efficiently. [PMID:12511654, PMID:15213240, PMID:9405336]
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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
The removal of a ubiquitin-like protein of the NEDD8 type from a protein. [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 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]
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 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 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 potassium ion is transported from one side of a membrane to the other. [GOC:mah]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
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]
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]
Any process that modulates the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle. [GOC:mtg_cell_cycle, PMID:17329565]
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]
A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins. [PMID:9191038]
Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0815340729]
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response. [GOC:bf, GOC:mcc, PMID:10966457, PMID:20223701, PMID:9191038]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
Interacting selectively and non-covalently with manganese (Mn) ions. [GOC:ai]
Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
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 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]
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]
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 repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix. [GOC:elh]
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [PMID:11563486]
The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair. [http://www.ultranet.com/~jkimball/BiologyPages/D/DNArepair.html]
Catalysis of the hydrolysis of 3'-phosphotyrosyl groups formed as covalent intermediates (in DNA backbone breakage) between DNA topoisomerase I and DNA. [PMID:10521354, PMID:16751265]
Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. [EC:3.1.4, GOC:curators]
Interacting selectively and non-covalently with single-stranded DNA. [GOC:elh, GOC:vw, PMID:22976174]
Interacting selectively and non-covalently with double-stranded DNA. [GOC:elh, GOC:vw]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of RNA splicing. [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]
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]
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 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 synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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]
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 portion of the photoreceptor cell cilium linking the photoreceptor inner and outer segments. It's considered to be equivalent to the ciliary transition zone. [GOC:cilia, PMID:15917207, PMID:22653444, PMID:8718680]
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 outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes. [GOC:cilia, ISBN:0824072820]
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 in which the identity of an animal organ is maintained. Identity is considered to be the aggregate of characteristics by which a structure is recognized. [GOC:tb]
Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light. [CL:0000210, GOC:bf, GOC:rl]
Interacting selectively and non-covalently with any enzyme. [GOC:jl]
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]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. [GOC:ai]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The linkage of cytochromes and other heme proteins to heme. [RESID:AA0134, RESID:AA0135]
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]
Catalysis of the reaction: holocytochrome c = apocytochrome c + heme. [EC:4.4.1.17]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Reactions triggered in response to the presence of a virus that act to protect the cell or organism. [GOC:ai]
Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade. [GOC:bf]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-6. [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]
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2. [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 exogenous double-stranded RNA stimulus. [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 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 the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. [GOC:jl, PMID:10891884]
Any process that 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 activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade. [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-6 production. [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 muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan. [GOC:add]
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptidoglycan stimulus. Peptidoglycan is a bacterial cell wall macromolecule. [GOC:add, ISBN:0721601464]
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 fungus. [GOC:hb]
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 an identical protein to form a homodimer. [GOC:jl]
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]
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. [GOC:jl, PMID:11584301]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. [ISBN:0198506732]
Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP. [GOC:dph, GOC:mah, GOC:tb]
Any process that activates or increases the activity of a GTPase. [GOC:jl, GOC:mah]
The directed movement of substances from late endosomes to the Golgi. [GOC:rb]
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]
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells. [CHEBI:33709, GOC:curators, ISBN:0198506732]
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 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]
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [ISBN:0198506732]
The larger of the two subunits of a mitochondrial ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site). [GOC:mcc]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The 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]
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 progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed. [GOC:dph, GOC:sdb_2009, GOC:tb]
The morphogenesis of the neural fold elevations that results in the movement of the tips of the elevations towards each other in order to fuse. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15806586]
The progression of the ventricular septum over time from its formation to the mature structure. [GOC:mtg_heart]
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]
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 process in which B cells acquire the specialized features of B-1a B cells. B-1a B cells are B-1 cells that express CD5 and arise from fetal liver precursors. [GOC:jal, 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]
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]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. [GOC:dph, GOC:tb]
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]
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. [GOC:kmv, SO:0000234]
A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein. [PMID:15571813, PMID:15688063]
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 nuclear import which involves only one organism. [GO_REF:0000089, GOC:jl, GOC:TermGenie]
The process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). [GOC:jl, GOC:txnOH, ISBN:0321000382]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Any process that 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 a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a 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]
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 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]
The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone. [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 FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. [GOC:go_curators]
Any molecular 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 involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. [GOC:bhm, PMID:22749910]
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 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]
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. [GOC:elh]
Any process that activates or increases the frequency, rate or extent of stem cell proliferation. [GOC:dph]
Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation. [GOC:dph, GOC:yaf]
Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:BHF, GOC:rl, PMID:22790009]
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]
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 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 whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate. [CL:0000187, GOC:devbiol]
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 stops, prevents, or reduces 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 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 neurogenesis, the origin and formation of neurons. [GOC:ai]
Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. [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 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 megakaryocyte differentiation. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. [GOC:go_curators]
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 the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. [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 ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. [GOC:mah]
Any process that activates or increases the frequency, rate or extent of the addition of a ubiquitin group to a histone protein. [GOC:mah]
The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone. [GOC:mah]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. [GOC:mah]
The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. [GOC:ecd, http://life.nthu.edu.tw/~g864204/dict-search1.htm]
The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
Any process that modulates the rate, frequency, or extent of primitive erythrocyte differentiation. Primitive erythrocyte differentiation occurs as part of the process of primitive hemopoiesis. [GOC:add, GOC:dph, GOC:tb]
Any process that modulates the frequency, rate or extent of the error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. [GOC:dph, GOC:jp, GOC:tb]
The multiplication or reproduction of cells, resulting in the expansion of a cell population. [GOC:mah, GOC:mb]
The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. [GOC:mah]
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
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 long non-coding RNA molecules transcribed from subtelomeric regions in most eukaryotes. Telomeric repeat-containing RNA (TERRA) molecules consist of subtelomeric-derived sequences and G-rich telomeric repeats. [GOC:BHF, GOC:BHF_telomere, GOC:dph, GOC:jbu, PMID:20655916]
Interacting selectively and non-covalently with an androgen receptor. [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 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 telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end. [GOC:jl, SO:0000624]
Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein. [GOC:mah, PMID:17550896]
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein. [PMID:16362057]
Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein. [GOC:mah]
Catalysis of the removal of a methyl group from a histone. [GOC:mah]
Catalysis of the removal of a methyl group from a substrate. [GOC:mah]
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]
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]
Interacting selectively and non-covalently with one of the p53 family of proteins. [GOC:hjd]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
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]
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 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 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]
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]
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 a cysteine-type endopeptidase activity involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263]
Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis, PMID:14744432, Wikipedia:Caspase]
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]
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 lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. [GOC:mah, ISBN:0198506732]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
The 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]
Interacting selectively and non-covalently with a specific domain of a protein. [GOC:go_curators]
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]
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: a beta-D-glucuronoside + H2O = an alcohol + D-glucuronate. [EC:3.2.1.31]
Catalysis of the hydrolysis of any O-glycosyl bond. [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 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 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 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-glucuronate + acceptor = UDP + acceptor beta-D-glucuronoside. [EC:2.4.1.17]
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 ribonucleoprotein complex containing both protein and messenger RNA (mRNA) molecules. [GOC:bf, PMID:15574591, PMID:21915786]
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 prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins. [GOC:sart, PMID:11113136]
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 cytoplasmic translation. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay. [GOC:mcc, GOC:TermGenie]
Any process that 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]
An mRNA destabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA. [GOC:dph, GOC:jh]
Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length. [GOC:dph, GOC:tb]
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:isa_complete]
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. [GOC:go_curators]
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 part of a ribosome. [GOC:go_curators]
Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome. [GOC:ai, GOC:vw]
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]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid. [GOC:clt, GOC:vw]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane. [ISBN:0198506732]
A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse.  They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including \thin\, \stubby\, \mushroom\, and \branched\, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity. [GOC:nln]
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. [http://www.bris.ac.uk/Depts/Synaptic/info/glutamate.html]
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 type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter. [ISBN:0198506732, ISBN:0716731363, ISBN:0815316194]
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 outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes. [GOC:cilia, ISBN:0824072820]
The behavior in which an organism produces sounds by a mechanism involving its respiratory system. [GOC:mah]
A process that modulates synaptic plasticity such that synapses are changed resulting in the decrease in the rate, or frequency of synaptic transmission at the synapse. [GOC:dgh, GOC:dph]
A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse. [GOC:dgh, GOC:dph]
Any process that activates, maintains or increases 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]
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]
Behavior in a fully developed and mature organism. [GOC:mah, ISBN:0877797099]
The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task). [GOC:curators, http://www.onelook.com/, ISBN:0582227089]
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 aggregation, arrangement and bonding together of a set of components to form a synapse.  This process ends when the synapse is mature (functional). [GOC:mah]
Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels. [GOC:bf, 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 chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. [ISBN:0198506732]
Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate. [EC:2.8.2, GOC:curators]
A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis. [ISBN:0815316194]
The 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]
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 histone deacetylase activity. [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:20497126]
The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances. [ISBN:0721662544]
Any process that activates or increases the rate or extent of progression through the cell cycle. [GOC:go_curators]
The series of events that restore integrity to a damaged tissue, following an injury. [GOC:bf, PMID:15269788]
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 multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. [PMID:11532962, PMID:11743026]
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 chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GOC:dph, GOC:go_curators, GOC:tb]
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 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 multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4. [GOC:bf, GOC:sp, PMID:12408863, PMID:12408864, PMID:20064375]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
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 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]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to 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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis. [GOC:go_curators]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
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 series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands. [GOC:ceb]
The initiation of the activity of the inactive enzyme MAP kinase (MAPK). [PMID:9561267]
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 surrounding the brush border. [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 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 neutral amino acids, amino acids with no net 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 a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. [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 active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. [GOC:mtg_transport, ISBN:0815340729, PMID:10839820]
Catalysis of the transfer of neutral amino acids from one side of a membrane to the other. Neutral amino acids have a pH of 7. [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: neurotransmitter(out) + Na+(out) = neurotransmitter(in) + Na+(in). [TC:2.A.22.-.-]
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 lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. [GOC:ai]
The process of removing one or more phosphate groups from a phosphatidylinositol. [ISBN:0198506732]
Catalysis of the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 3-phosphate + phosphate. [GOC:mah]
A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8. [PMID:10637607, PMID:17337012]
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 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]
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 collagen heterotrimer containing type IX alpha chains in alpha1(IX)alpha2(IX)alpha3(IX) trimers; type IX collagen triple helices associate to form a structure that links glycosaminoglycans to type II collagen fibrils. [ISBN:0721639976]
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]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The network of interconnected tubular and cisternal structures located 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]
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 directed movement of proteins within cells. [GOC:tb]
The chemical reactions and pathways resulting in the formation of dermatan sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are dermatan sulfate (chondroitin sulfate B). Dermatan sulfate is a glycosaminoglycan with repeats consisting of beta-(1,4)-linked L-iduronyl-beta-(1,3)-N-acetyl-D-galactosamine 4-sulfate units. [GOC:ai]
The chemical reactions and pathways resulting in the formation of chondroitin sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. [GOC:ai]
Any process that activates or increases the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
The chemical reactions and pathways involving chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. They usually occur linked to a protein to form proteoglycans. Two subgroups exist, one in which the sulfate is on the 4-position (chondroitin sulfate A) and the second in which it is in the 6-position (chondroitin sulfate C). They often are polydisperse and often differ in the degree of sulfation from tissue to tissue. The chains of repeating disaccharide are covalently linked to the side chains of serine residues in the polypeptide backbone of a protein by a glycosidic attachment through the trisaccharide unit galactosyl-galactosyl-xylosyl. Chondroitin sulfate B is more usually known as dermatan sulfate. [GOC:mah, ISBN:0198506732]
The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues. [GOC:mah, ISBN:0198506732, ISBN:0198547684, RESID:AA0210]
The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. [ISBN:0192800981]
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]
Increases the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule. [GOC:mah]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the reaction: UDP-glucuronate + acceptor = UDP + acceptor beta-D-glucuronoside. [EC:2.4.1.17]
Catalysis of the reaction: UDP-glucuronate + 3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein = UDP + 3-beta-D-glucuronosyl-3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein. [EC:2.4.1.135]
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 collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. [GOC:lh]
A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins. [GOC:mah, GOC:mtg_muscle, http://en.wikipedia.org/wiki/Gap_junction, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_g.html, ISBN:0815332181, PMID:22366062]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell.  Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. [GOC:dos, GOC:mah]
The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
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 inadequate blood supply. [GOC:hjd]
Enables the transport of a solute across a membrane via a large pore, un-gated channel. Examples include gap junctions, which transport substances from one cell to another; and porins which transport substances in and out of bacteria, mitochondria and chloroplasts. [GOC:mtg_transport, ISBN:0815340729]
Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. [GOC:mtg_transport, ISBN:0815340729, TC:1.-.-.-.-]
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]
The portion of sarcoplasmic reticulum devoted to calcium ion storage and calcium ion release. [GOC:mtg_muscle]
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 directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore. [GOC:isa_complete]
Any process that modulates the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. [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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. [GOC:ai, GOC:pr]
Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity. [GOC:bf]
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 stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein. [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 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 results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GOC:sl]
Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates. [CHEBI:16646, GOC:mah]
The region between the inner and outer lipid bilayers of the mitochondrial envelope. [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 metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
The process of assisting in the correct noncovalent folding of newly formed polypeptides or folding intermediates of polypeptides that have exited the ribosome and/or have been stabilized and transferred by other chaperone proteins. This process could involve several cycles of ATP hydrolysis. [GOC:rb]
The import of proteins into the space between the inner and outer mitochondrial membranes. [ISBN:0716731363]
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein. [GOC:isa_complete]
Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds. [MetaCyc:DISULFOXRED-RXN]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands. [GOC:dgh]
A series of molecular signals mediated by a steroid hormone binding to a receptor. [PMID:12606724]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with zinc (Zn) ions. [GOC:ai]
Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene. [GOC:jl, ISBN:0198506732]
Combining with retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. Retinoic acid is one of the forms of vitamin A. [GOC:signaling, PMID:1328967]
Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function. [GOC:signaling, PMID:14708019]
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:curators, GOC:txnOH]
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
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 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 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]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. [GOC:mah]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of glucose. [GOC:jl]
The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation. [GOC:mah, PMID:12042763]
Interacting selectively and non-covalently with a phosphorylated protein. [GOC:ai]
Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation. [GOC:mah]
Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. [GOC:jl]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II. [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]
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 ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
Any process that stops, prevents or reduces the frequency, rate or extent of neuron migration. [GOC:obol]
Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation. [GOC:obol]
Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA. [GOC:dph]
Any process that activates or increases 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 pri-miRNA transcription from RNA polymerase II promoter. [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
Any process involved in the balance between food intake (energy input) and energy expenditure. [GOC:yaf, PMID:15919751]
The process in which a CD4-positive, alpha-beta T cell becomes committed to becoming a T-helper 17 cell, a CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive that produces IL-17. [CL:0000899, GOC:BHF, GOC:ebc]
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 STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes. [GOC:BHF, GOC:dph, PMID:11445442]
The series of molecular signals generated as a consequence of growth hormone receptor binding to its physiological ligand. [GOC:BHF, GOC:dph, PMID:11445442]
Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food. [GOC:BHF, GOC:dph, GOC:tb]
The process in which neuroepithelial cells of the neural tube give rise to radial glial cells, specialized bipotential progenitors cells of the brain. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GOC:dph]
Any process that modulates the rate or extent of progression through the cell cycle. [GOC:ai, GOC:dph, GOC:tb]
The process in which a relatively unspecialized cell acquires the specialized features of an astrocyte. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function. [GOC:vp, PMID:15139015]
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 glycolysis. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway. [GOC:go_curators]
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a leptin stimulus. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. It plays a key role in regulating energy intake and energy expenditure, including appetite and metabolism]. [GOC:yaf]
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a leptin stimulus. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. It plays a key role in regulating energy intake and energy expenditure, including appetite and metabolism. [GOC:yaf]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. [GOC:jl, ISBN:0321000382]
The 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 involved in the maintenance of an internal steady state of glucose within an organism or cell. [GOC:go_curators]
Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size. [GOC:dph, GOC:ems, GOC:tb]
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]
A series of molecular signals initiated by the binding of leptin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. [GOC:mah, GOC:signaling, GOC:yaf]
Any process that 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 hormone stimulus. [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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen. [GOC:mah, ISBN:0911910123]
Any series of molecular signals initiated by a ligand binding to an receptor located within a cell. [GOC:bf, GOC:mah]
A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. [GOC:jl, http://en.wikipedia.org/wiki/Sexual_reproduction, ISBN:0387520546]
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 process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [ISBN:0198506732]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
Any process that 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 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 immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]
The directed movement of a protein from the cytoplasm to the nucleus. [GOC:jl]
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 process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms. [GOC:go_curators]
A homeostatic process in which an organism modulates its internal body temperature. [GOC:jl]
The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with a 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]
Interacting selectively and non-covalently with DNA that is assembled into chromatin. [GOC:mah]
Interacting selectively and non-covalently with any protein phosphatase. [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 a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. [GOC:signaling, GOC:txnOH]
Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. [GOC:go_curators]
Interacting selectively and non-covalently with a 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 an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription. [GOC:txnOH]
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter. [GOC:txnOH]
Interacting selectively and non-covalently with a 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]
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 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 focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing. [GOC:clt, PMID:12730603]
Any process that activates or increases the activity of an enzyme. [GOC:ebc, GOC:jl, GOC:tb, GOC:vw]
Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening. [GOC:krc, PMID:15225542, PMID:15225544]
Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length. [GOC:krc]
Binds to and modulates the activity of an enzyme. [GOC:dph, GOC:mah, GOC:tb]
Binds to and increases the activity of an enzyme. [GOC:dph, GOC:mah, GOC:tb]
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. [GOC:kmv, SO:0000234]
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). [ISBN:0198506732]
The process in which an antigen-presenting cell expresses a peptide antigen of endogenous 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 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 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]
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 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]
Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. [GOC:dph, GOC:mtg_cardio, ISBN:0721643949]
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell.  Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. [GOC:dos, GOC:mah]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
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 N-terminal amino acid residues from in a polypeptide chain. [GOC:jl, ISBN:0198506732]
A transmembrane protein complex that is involved in protein folding in the endoplasmic reticulum. In S. cerevisiae, it has six members: EMC1, EMC2, AIM27, EMC4, KRE27, and EMC6. [GOC:dgf, PMID:19325107]
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 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 conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. [PMID:11687631, PMID:11742990, PMID:11805083, PMID:12488447, PMID:18508253, PMID:18838538]
An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters. [GOC:bf, GOC:krc, PMID:10779516, PMID:11279013, PMID:15284901, PMID:16568949, PMID:21810179]
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 ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. [GOC:elh, PMID:20404130]
Any process involved in the maintenance of an internal steady state of lipid within an organism or cell. [GOC:BHF, GOC:rl]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Any process that results in a change in state or activity of a cell (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 transcription of the final group of viral genes of the viral life cycle, following middle transcription, or where middle transcription doesn't occur, following early transcription. Involves the transcription of genes encoding structural proteins. [GOC:bf, GOC:jh2, 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 ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. [GOC:hb]
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 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]
Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter. [GOC:krc]
The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer. [GOC:ai]
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl]
Interacting selectively and non-covalently with 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 the enzyme histone deacetylase. [GOC:jl]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
Interacting selectively and non-covalently with 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 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]
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 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 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]
The homotypic fusion of endocytic vesicles to form or add to an early endosome. [PMID:11964142, PMID:9422733]
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 substances from endosomes to lysosomes. [GOC:ai, ISBN:0716731363]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The directed movement of 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]
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 SMAD signaling protein. [GOC:ai]
Interacting selectively and non-covalently with the transforming growth factor beta receptor. [GOC:ai]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
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]
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 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 signal transduction mediated by the ERK1 and ERK2 cascade. [GOC:add, ISBN:0121245462, ISBN:0896039986]
The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head. [GOC:dph]
Any process that modulates the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B. [GOC:ai]
Any process that activates or increases angiogenesis. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. [GOC:go_curators]
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals. [GOC:mah]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. [CL:0000738, GOC:add, PMID:16551264]
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate. [GOC:ai]
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 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 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]
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]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
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 a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus. [GOC:pr, GOC:TermGenie]
Any process that activates or increases the frequency, rate or extent of vasoconstriction. [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 hormone stimulus. [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]
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 regulation of blood pressure mediated by the signaling molecule vasopressin. Vasopressin is produced in the hypothalamus, and affects vasoconstriction, and renal water transport. [GOC:mtg_cardio, ISBN:0721643949]
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]
Combining with vasopressin to initiate a change in cell activity. [GOC:ai]
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]
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 lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. [GOC:go_curators]
The chemical reactions and pathways resulting in the breakdown 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 involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. [GOC:ma]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. [ISBN:0198506732]
Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate. [EC:3.1.1.4]
Catalysis of the hydrolysis of a glycerophospholipid. [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/]
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 series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP). [GOC:mtg_apoptosis, GOC:yaf, PMID:11919192, PMID:17340152, PMID:18852119]
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 assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts. [GOC:ai]
Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. [GOC:ai]
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The stopping, prevention, or reduction in frequency, rate or extent of protein kinase activity as a result of regulating the phosphorylation status of that protein kinase. [GOC:jl]
Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
The removal of phosphoric residues from peptidyl-O-phospho-L-threonine to form peptidyl-threonine. [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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GOC:sl]
Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine. [GOC:mah]
Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules. [GOC:dph, GOC:pf, GOC:tb]
Any process that activates or increases the frequency, rate or extent of epithelial cell migration. [GOC:BHF, GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
The process of removing one or more phosphoric residues from a protein. [GOC:hb]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge. [GOC:jl]
Catalysis of the reaction: protein serine/threonine phosphate + H2O = protein serine/threonine + phosphate, dependent on the presence of calcium-bound calmodulin. [GOC:mah, PMID:15359118]
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 serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate. [GOC:bf]
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 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 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 initiates the activity of an inactive GTPase through the replacement of GDP by GTP. [GOC:dph, GOC:mah, GOC:tb]
The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis. [GOC:tb, GOC:vw]
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]
The replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized. [GOC:ai]
Any process that modulates the frequency, rate or extent of Rho protein signal transduction. [GOC:bf]
The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
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]
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]
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. [GOC:mah, GOC:pz]
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 in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. [CL:0000034, GOC:isa_complete]
The process 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]
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 stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation. [GOC:go_curators]
Any process that stops, prevents, or reduces the frequency, rate or extent of keratinocyte differentiation. [GOC:go_curators]
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
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 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 leukocyte migration. [GOC:add]
Any process that stops, prevents, or reduces the rate or extent of cell adhesion to the extracellular matrix. [GOC:hjd]
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 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 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 process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. [GOC:dph, GOC:tb]
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]
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. [GOC:kmv, SO:0000234]
A structure lying external to one or more cells, which provides structural support for cells or tissues. [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. [ISBN:0198547684]
A type of extracellular matrix found in interstitial connective tissue, characterized by the presence of fibronectins, proteoglycans, and types I, III, V, VI, VII and XII collagens. [PMID:8450001]
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]
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. [GOC:jl, GOC:mtg_apoptosis]
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 hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. [GOC:bf, GOC:mah]
The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface. [GOC:dph]
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [GOC:jl, ISBN:0815332181]
Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which 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]
Interacting selectively and non-covalently with any protease or peptidase. [GOC:hjd]
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 lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
The lipid bilayer surrounding a peroxisome. [GOC:mah]
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
The process whose specific outcome is the progression of a Sertoli cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a Sertoli cell fate. [GOC:dph]
The chemical reactions and pathways involving medium-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. A medium-chain fatty acid is a fatty acid with a chain length of between C6 and C12. [CHEBI:61907, GOC:pm]
The chemical reactions and pathways involving very long-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a medium-chain fatty-acyl group. A very long-chain fatty acid is a fatty acid which has a chain length greater than C22. [CHEBI:61910, GOC:pm]
The chemical reactions and pathways involving estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants. [ISBN:0198506732]
The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics. [ISBN:0198506732]
A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively). [GOC:mah, ISBN:0198506732, MetaCyc:FAO-PWY]
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. [CL:0000062, GO_REF:0000034, GOC:jid]
The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22. [CHEBI:27283, GOC:hjd]
Catalysis of the reaction: a 17-beta-hydroxysteroid + NAD+ = a 17-oxosteroid + NADH + H+. [PMID:17074428]
Interacting selectively and non-covalently with an identical protein to form a homodimer. [GOC:jl]
Catalysis of the reaction: a long-chain (3S)-3-hydroxyacyl-CoA = a long-chain trans-2-enoyl-CoA + H2O. A long-chain acyl-CoA is an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms. [EC:4.2.1.74]
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: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+). [EC:1.1.1.35]
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 attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GOC:hb, GOC:pf]
Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. [ISBN:0198506732]
Interacting selectively and non-covalently with an RNA molecule or a portion thereof. [GOC:mah]
Interacting selectively and non-covalently with any nucleic acid. [GOC:jl]
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 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 characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature. [CL:0000540, GOC:go_curators]
An ion channel complex through which sodium ions pass. [GOC:mah]
An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed. [GOC:mh]
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]
A sodium channel in a cell membrane whose opening is governed by the membrane potential. [ISBN:0198506732]
Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity. [GOC:obol]
A cardiac conduction process that modulates the frequency or rate of heart contraction. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
The process in which Purkinje myocyte 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 cardiac muscle cell membrane potential changes in the depolarizing direction from the negative resting potential towards the positive membrane potential that will be the peak of the action potential. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
An action potential that occurs in a cardiac muscle cell and is involved in its contraction. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles. [GOC:dph]
Any process that modulates the establishment or extent of a membrane potential in the depolarizing direction away from the resting potential in an atrial cardiomyocyte. [GOC:dph, GOC:tb]
Any process that modulates the establishment or extent of a membrane potential in the polarizing direction towards the resting potential in a ventricular cardiomyocyte. [GOC:BHF, GOC:dph, GOC:mtg_cardiac_conduct_nov11, GOC:tb]
Any process that modulates the potential difference across a post-synaptic membrane. [GOC:dph, GOC:ef]
Muscle contraction of cardiac muscle tissue. [GOC:dph]
The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential. [GOC:dh, Wikipedia:Depolarization]
Self-propelled movement of a cell or organism from one location to another. [GOC:dgh]
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:vw]
The process in which the migration of an axon growth cone of a neuron that is part of the corticospinal tract is directed from the cerebral cortex layer V to the spinal cord dorsal funiculus in response to a combination of attractive and repulsive cues. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:9878731]
The propagation of an action potential along an axon, away from the soma. [GOC:isa_complete]
Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). [GOC:dph, GOC:tb]
Any process that increases the frequency, rate or extent of 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 chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues. [ISBN:0878932437]
The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Enables the transmembrane transfer of a sodium ion by a voltage-gated channel through the plasma membrane of a Purkinje myocyte contributing to the depolarization phase of an action potential. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
Enables the transmembrane transfer of a sodium ion by a voltage-gated channel through the plasma membrane of a cardiac muscle cell contributing to the depolarization phase of an action potential. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
Stops, prevents, or reduces the activity of a sodium channel. [GOC:mah]
Modulates the activity of a sodium channel. [GOC:mah]
Enables the transmembrane transfer of a sodium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded. [GOC:mtg_transport, ISBN:0815340729]
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 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]
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GOC:go_curators]
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. [GOC:go_curators, GOC:txnOH]
The 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 conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication. [GOC:elh]
Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain. [ISBN:0815316194]
Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues. [GOC:BioGRID, GOC:dph, GOC:mah, GOC:tb, PMID:22863777]
Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
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 hydrolysis of any acid anhydride which contains phosphorus. [GOC:jl]
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]
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 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]
Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. [GOC:dph, GOC:tb]
Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver. [ISBN:0198506732]
Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. [GOC:jl, ISBN:0198506732]
Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme. [GOC:ai]
A 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]
Interacting selectively and non-covalently with an identical protein or proteins. [GOC:jl]
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. [ISBN:0716731363]
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. [GOC:hjd, GOC:jl]
That part of the nuclear content other than the chromosomes or the nucleolus. [GOC:ma, ISBN:0124325653]
Any process that activates or increases the activity of a GTPase. [GOC:jl, 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 or reduces the rate of GTP hydrolysis by a GTPase. [GO_REF:0000058, GOC:mah, GOC:rb, GOC:TermGenie, PMID:16143306, PMID:24335649]
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. [GOC:go_curators, GOC:mtg_signaling_feb11]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP. [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 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 component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A 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]
A process that modulates synaptic plasticity such that synapses are changed resulting in the decrease in the rate, or frequency of synaptic transmission at the synapse. [GOC:dgh, GOC:dph]
A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse. [GOC:dgh, GOC:dph]
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other [GOC:dph, GOC:jid]
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. [GOC:vw]
The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. [GOC:ai]
Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. [GOC:ceb, GOC:mah]
The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [GOC:ai]
Interacting selectively and non-covalently with sodium ions (Na+). [GOC:mah]
Interacting selectively and non-covalently with potassium (K+) ions. [GOC:mah]
Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Ca2+(in) + K+(in) + Na+(out) = Ca2+(out) + K+(out) + Na+(in). [TC:2.A.19.4.1]
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]
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. [GOC:BHF, GOC:mah, GOC:vesicles, PMID:15908444, PMID:17641064, PMID:19442504, PMID:19498381, PMID:22418571, PMID:24009894]
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GOC:giardia, ISBN:0198506732]
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]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. [ISBN:0124325653, ISBN:0815316208]
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 highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. [GOC:dph, GOC:mtg_lung]
The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle. [CL:0000737, GOC:ai]
Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue. [GOC:isa_complete]
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]
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 cell death by apoptotic process in neurons. [GOC:go_curators, GOC:mtg_apoptosis]
The transfer of information from one cell to another, where an endocrine hormone is transported from the signal-producing cell to the receiving cell via the circulatory system (via blood, lymph or cerebrospinal fluid). The signaling cell and the receiving cell are often distant to each other. [GOC:mtg_signaling_feb11, ISBN:0199264678, ISBN:3527303782]
Any process that activates or increases the frequency, rate or extent of Rac protein signal transduction. [GOC:bf]
Any process that modulates 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 affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation. [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]
The process aimed at the progression of an astrocyte that resides in the forebrain, from initial commitment of the cell to its fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function. [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06]
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 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]
Any process that activates or increases the rate or extent of cell proliferation. [GOC:go_curators]
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]
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]
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 protein complex (a complex of two or more proteins that may include other nonprotein molecules). [GOC:mah]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
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 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 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]
A small (70-100 nm) cytoplasmic granule that contains a number of centrosomal proteins; centriolar satellites traffic toward microtubule minus ends and are enriched near the centrosome. [GOC:BHF, PMID:10579718, PMID:12403812]
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 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]
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 multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species. [GOC:clt, PMID:12134075]
Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. [GOC:tb]
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. [GOC:BHF, GOC:mah]
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2]
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
Interacting selectively and non-covalently with an identical protein or proteins. [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 involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation. [GOC:ai]
The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation). [ISBN:0198506732]
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 introducing a phosphate group to a serine residue of the STAT3 protein. [GOC:jl, 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 phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine. [RESID:AA0038]
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 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 frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [GOC:dph, GOC:tb]
A series of molecular signals 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 process of introducing a phosphate group on to a protein. [GOC:hb]
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. [GOC:go_curators, GOC:txnOH]
The cellular synthesis of RNA on a template of DNA. [GOC:jl, GOC:txnOH]
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]
Interacting selectively and non-covalently with any metal ion. [GOC:ai]
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 ubiquitin protein ligase enzyme, any of the E3 proteins. [GOC:vp]
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. [ISBN:0198506732]
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. [ISBN:0198506732]
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. [ISBN:0198506732]
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. [ISBN:0198506732]
Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli. [GOC:ma, ISBN:0198547684]
Catalysis of the 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 magnesium (Mg) ions. [GOC:ai]
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. [GOC:mah, ISBN:0198547684]
The 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 process in which one or more ubiquitin groups are added to a protein. [GOC:ai]
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 stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling. [GOC:bf]
Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity. [GOC:bf]
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 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 protein kinase C (PKC). PKC is activated by second messengers including diacylglycerol (DAG). [GOC:mah, GOC:signaling]
Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity. [GOC:go_curators]
Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein. [GOC:ai]
The lipid bilayer surrounding a recycling endosome. [GOC:jid, GOC:rph, PMID:10930469, PMID:15601896, PMID:16246101]
Cytoplasm situated near, or occurring around, the nucleus. [GOC:jid]
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 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]
That part of the plasma membrane found in the ciliary pocket (also called flagellar pocket). [GOC:cilia, GOC:mb]
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]
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. [ISBN:0198547684]
Any process that modulates the frequency, rate or extent of cardiac conduction. [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rph, GOC:TermGenie, PMID:12967627]
Any process that modulates the frequency, rate or extent of Golgi organization. [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:17562788]
Any process that activates or increases the frequency, rate or extent of voltage-gated calcium channel activity. [GOC:BHF, GOC:TermGenie]
The directed movement of substances from the Golgi to lysosomes. [GOC:ascb_2009, GOC:dph, GOC:tb]
Any process that modulates the establishment or extent of a membrane potential in a cardiac muscle cell (a cardiomyocyte). A membrane potential is the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
The process of directing proteins towards the plasma membrane; usually uses signals contained within the protein. [GOC:mah]
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 modulates the frequency, rate or extent of cardiac muscle contraction. [GOC:ecd]
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 directed movement of substances from early endosomes to the Golgi. [GOC:rb]
The directed movement of membrane-bounded vesicles from recycling endosomes back to the plasma membrane where they are recycled for further rounds of transport. [GOC:ecd, PMID:16473635]
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]
Interacting selectively and non-covalently with GTP, guanosine triphosphate. [GOC:ai]
Interacting selectively and non-covalently with calcium ions (Ca2+). [GOC:ai]
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. [GOC:dos, GOC:go_curators]
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. [GOC:dos, GOC:mah, ISBN:0815316194]
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor. [GOC:mah, ISBN:0815316194]
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]
Combining with the tridecapeptide neurotensin to initiate a G-protein mediated change in cell activity. A G-protein is a signal transduction molecule that alternates between an inactive GDP-bound and an active GTP-bound state. [PMID:10390649]
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]
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 structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. [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]