Gene Ontology Ontology Comparison Report ========================== Files used: - file 1 (old): go-2011-11-19.obo; date: 18:11:2011 17:55; CVS revision: 1.2388 - file 2 (new): go-2011-11-26.obo; date: 24:11:2011 22:03; CVS revision: 1.2403 NEW TERMS ========= ID name namespace GO:0001196 regulation of mating-type specific transcription from RNA polymerase II promoter biological_process GO:0001197 positive regulation of mating-type specific transcription from RNA polymerase II promoter biological_process GO:0001198 negative regulation of mating-type specific transcription from RNA polymerase II promoter biological_process GO:0001199 metal ion regulated sequence-specific DNA binding RNA polymerase transcription factor activity molecular_function GO:0001200 metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity molecular_function GO:0001201 metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity molecular_function GO:0001202 copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity molecular_function GO:0001203 zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity molecular_function GO:0001204 metal ion regulated bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity molecular_function GO:0036038 tectonic complex cellular_component GO:0036039 curcumin metabolic process biological_process GO:0036040 curcumin catabolic process biological_process GO:0036041 long-chain fatty acid binding molecular_function GO:0036042 long-chain fatty acyl-CoA molecular_function GO:0097186 amelogenesis biological_process GO:0097187 dentinogenesis biological_process GO:0097188 dentin mineralization biological_process GO:0097189 apoptotic body cellular_component GO:0097190 apoptotic signaling pathway biological_process GO:0097191 extrinsic apoptotic signaling pathway biological_process GO:0097192 extrinsic apoptotic signaling pathway in absence of ligand biological_process GO:0097193 intrinsic apoptotic signaling pathway biological_process GO:0097194 execution phase of apoptosis biological_process OBSOLETIONS =========== None TERM MERGES =========== GO:0034619, cellular chaperone-mediated protein complex assembly was merged into GO:0051131, chaperone-mediated protein complex assembly TERM CHANGES ============ GO:0006351 : transcription, DNA-dependent + subset: goslim_pombe GO:0006366 : transcription from RNA polymerase II promoter - subset: goslim_pombe GO:0006636 : unsaturated fatty acid biosynthetic process + synonym: "polyunsaturated fatty acid biosynthesis" NARROW [GOC:yaf, MetaCyc:PWY-762] GO:0006915 : apoptotic process - name: apoptosis + name: apoptotic process - def: A form of programmed cell death that begins when a cell receives internal or external signals that trigger the activity of proteolytic caspases, proceeds through a series of characteristic stages typically including rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), and plasma membrane blebbing (but maintenance of its integrity until the final stages of the process), and ends with the death of the cell. + def: 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 pathways) which typically lead to 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. The process ends when the cell has died. The process is divided into a signaling pathway phase and into an execution phase, which is triggered by the former. + synonym: "cell suicide" BROAD [] + synonym: "cellular suicide" BROAD [] + synonym: "apoptosis" NARROW [] GO:0007165 : signal transduction - def: 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, and 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. + def: 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. GO:0007166 : cell surface receptor linked signaling pathway - def: Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell. + def: 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. GO:0007186 : G-protein coupled receptor signaling pathway - def: Any series of molecular signals initiated by an extracellular signal combining with a receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. 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 and ends with regulation of a downstream cellular process, e.g. transcription. + def: Any 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. GO:0007194 : negative regulation of adenylate cyclase activity + is_a: GO:0030818 GO:0007532 : regulation of mating-type specific transcription, DNA-dependent - name: regulation of transcription, mating-type specific + name: regulation of mating-type specific transcription, DNA-dependent - def: Any mating-type specific process that modulates the frequency, rate or extent of transcription. + def: Any mating-type specific process that modulates the frequency, rate or extent of cellular DNA-dependent transcription. GO:0008219 : cell death - def: A biological process that results in permanent cessation of all vital functions of a cell. + def: Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as \"apoptotic bodies\"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo. GO:0012501 : programmed cell death - def: Cell death resulting from activation of endogenous cellular processes. + def: A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. + synonym: "PCD" EXACT [] GO:0012507 : ER to Golgi transport vesicle membrane + synonym: "ER to Golgi constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0012508 : Golgi to ER transport vesicle membrane + synonym: "Golgi to ER constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0012509 : inter-Golgi transport vesicle membrane + synonym: "inter-Golgi transport constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0012510 : trans-Golgi network transport vesicle membrane + synonym: "trans-Golgi network constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0015114 : phosphate ion transmembrane transporter activity + synonym: "phosphate transmembrane transporter activity" EXACT [GOC:vw] GO:0030133 : transport vesicle + synonym: "constitutive secretory pathway transport vesicle" EXACT [] GO:0030134 : ER to Golgi transport vesicle + synonym: "ER to Golgi constitutive secretory pathway transport vesicle" EXACT [] GO:0030140 : trans-Golgi network transport vesicle + synonym: "trans-Golgi network constitutive secretory pathway transport vesicle" EXACT [] GO:0030141 : secretory granule - name: stored secretory granule + name: secretory granule GO:0030142 : Golgi to ER transport vesicle + synonym: "Golgi to ER constitutive secretory pathway transport vesicle" EXACT [] GO:0030143 : inter-Golgi transport vesicle + synonym: "inter-Golgi transport constitutive secretory pathway transport vesicle" EXACT [] GO:0030175 : filopodium - synonym: "microspike" EXACT [] GO:0030658 : transport vesicle membrane + synonym: "constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0031234 : extrinsic to internal side of plasma membrane + comment: Consider also annotating to 'cell cortex ; GO:0005938'. GO:0031931 : TORC1 complex - def: A protein complex that contains the TOR (target of rapamycin) serine/threonine kinase and mediates temporal control of cell growth via regulation of translation, transcription, ribosome biogenesis, nutrient transport, and autophagy. In Saccharomyces, the complex contains Kog1p, Lst8p, Tco89p, and either Tor1p or Tor2p; in mammals the complex contains orthologs of the yeast proteins. + def: A protein complex that contains at least TOR (target of rapamycin) and Raptor (regulatory-associated protein of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of S6K. In Saccharomyces, the complex contains Kog1p, Lst8p, Tco89p, and either Tor1p or Tor2p. + synonym: "dTOR/dRaptor complex" NARROW [PMID:17183368] + synonym: "mTORC1" NARROW [PMID:18765678, PMID:21548787] + synonym: "TORC1" EXACT [PMID:21548787] + synonym: "rapamycin and nutrient-sensitive TOR complex" EXACT [PMID:21548787] + synonym: "dTORC1" NARROW [PMID:17183368] GO:0031932 : TORC2 complex - def: A protein complex that contains the TOR (target of rapamycin) serine/threonine kinase and mediates spatial control of cell growth via regulation of actin cytoskeleton polarization. In Saccharomyces, the complex contains Avo1p, Avo2p, Tsc11p, Lst8p, Bit61p, Slm1p, Slm2p, and Tor2p; in mammals the complex contains orthologs of the yeast proteins. + def: A protein complex that contains at least TOR (target of rapamycin) and Rictor (rapamycin-insensitive companion of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of PKB (also called AKT). In Saccharomyces, the complex contains Avo1p, Avo2p, Tsc11p, Lst8p, Bit61p, Slm1p, Slm2p, and Tor2p. + synonym: "TORC2" EXACT [PMID:21548787] + synonym: "mTORC2" NARROW [PMID:20496258, PMID:21548787] + synonym: "rapamycin and nutrient-insensitive TOR complex" EXACT [PMID:21548787] GO:0034505 : tooth mineralization - def: The process in which calcium salts are deposited into calcareous tooth structures such as dental enamel, dentine and cementum. + def: The process in which calcium salts are deposited into calcareous tooth structures such as dental enamel, dentin and cementum. GO:0035727 : lysophosphatidic acid binding - is_a: GO:0005504 + is_a: GO:0036041 GO:0038023 : signaling receptor activity - def: Receiving an extracellular or intracellular signal and transmitting the signal to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. + def: Receiving a signal and transmitting the signal in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. - comment: Note that this term and its child terms are intended for receptors that are directly coupled to a signal transduction pathway. This term should therefore not be used to annotate decoy receptors and other proteins that bind a signal but do not pass the signal on. For receptors that mediate transport of a substance into the cell by receptor-mediated endocytosis, consider instead the term 'cargo receptor activity ; GO:0038024' and its children. + comment: Note that this term and its child terms are intended for receptors that are directly coupled to a signal transduction pathway. This term should therefore not be used to annotate decoy receptors and other proteins that bind a signal but do not pass the signal on. This term can be used to annotate dependence receptors that transduce a signal when a ligand is withdrawn (in this case, signal withdrawal is considered to be the initiating signal), or receptors that signal at a basal level in the absence of a bound agonist. For receptors that mediate transport of a substance into the cell by receptor-mediated endocytosis, consider instead the term 'cargo receptor activity ; GO:0038024' and its children. GO:0038035 : G-protein coupled receptor signaling in absence of ligand + is_a: GO:0007186 GO:0042475 : odontogenesis of dentin-containing tooth - name: odontogenesis of dentine-containing tooth + name: odontogenesis of dentin-containing tooth - def: The process whose specific outcome is the progression of a dentine-containing tooth over time, from its formation to the mature structure. A dentine-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and are composed mainly of dentine, a dense calcified substance, covered by a layer of enamel. + def: 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. + comment: Note that placoid scales found in the cartilaginous fishes presumably develop through the same processes, but are found on the dermis, rather than in the mouth or pharynx. See http://en.wikipedia.org/wiki/Placoid_scale#Placoid_scales. - synonym: "odontogenesis of dentin-containing tooth" EXACT [GOC:mah] + synonym: "odontogenesis of dentine-containing tooth" EXACT [GOC:mah] GO:0042487 : regulation of odontogenesis of dentin-containing tooth - name: regulation of odontogenesis of dentine-containing tooth + name: regulation of odontogenesis of dentin-containing tooth - synonym: "regulation of odontogenesis of dentin-containing tooth" EXACT [GOC:mah] + synonym: "regulation of odontogenesis of dentine-containing tooth" EXACT [GOC:mah] GO:0042488 : positive regulation of odontogenesis of dentin-containing tooth - name: positive regulation of odontogenesis of dentine-containing tooth + name: positive regulation of odontogenesis of dentin-containing tooth - synonym: "positive regulation of odontogenesis of dentin-containing tooth" EXACT [GOC:mah] + synonym: "positive regulation of odontogenesis of dentine-containing tooth" RELATED [] GO:0042489 : negative regulation of odontogenesis of dentin-containing tooth - name: negative regulation of odontogenesis of dentine-containing tooth + name: negative regulation of odontogenesis of dentin-containing tooth - synonym: "negative regulation of odontogenesis of dentin-containing tooth" EXACT [GOC:mah] + synonym: "negative regulation of odontogenesis of dentine-containing tooth" RELATED [] GO:0042981 : regulation of apoptotic process - name: regulation of apoptosis + name: regulation of apoptotic process - def: Any process that modulates the occurrence or rate of cell death by apoptosis. + def: Any process that modulates the occurrence or rate of cell death by apoptotic process. + comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. + synonym: "regulation of apoptosis" NARROW [] GO:0043065 : positive regulation of apoptotic process - name: positive regulation of apoptosis + name: positive regulation of apoptotic process - def: Any process that activates or increases the frequency, rate or extent of cell death by apoptosis. + def: Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. + comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. + synonym: "positive regulation of apoptosis" NARROW [] GO:0043066 : negative regulation of apoptotic process - name: negative regulation of apoptosis + name: negative regulation of apoptotic process - def: Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptosis. + def: Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. + comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. + synonym: "negative regulation of apoptosis" NARROW [] GO:0045762 : positive regulation of adenylate cyclase activity + is_a: GO:0030819 GO:0045894 : negative regulation of mating-type specific transcription, DNA-dependent - name: negative regulation of transcription, mating-type specific + name: negative regulation of mating-type specific transcription, DNA-dependent - def: Any mating-type specific process that stops, prevents or reduces the rate of transcription. + def: Any mating-type specific process that stops, prevents or reduces the rate of cellular DNA-dependent transcription. GO:0045895 : positive regulation of mating-type specific transcription, DNA-dependent - name: positive regulation of transcription, mating-type specific + name: positive regulation of mating-type specific transcription, DNA-dependent - def: Any mating-type specific process that activates or increases the rate of transcription. + def: Any mating-type specific process that activates or increases the rate of cellular DNA-dependent transcription. GO:0046848 : hydroxyapatite binding - def: Interacting selectively and non-covalently with hydroxyapatite, the calcium phosphate mineral of formula Ca10(PO4)6(OH)2 found both in rocks of nonorganic origin and as a component of bone and dentine. + def: Interacting selectively and non-covalently with hydroxyapatite, the calcium phosphate mineral of formula Ca10(PO4)6(OH)2 found both in rocks of nonorganic origin and as a component of bone and dentin. GO:0051131 : chaperone-mediated protein complex assembly + alt_id: GO:0034619 + synonym: "cellular chaperone-mediated protein complex assembly" EXACT [] GO:0060199 : clathrin sculpted glutamate transport vesicle + synonym: "clathrin sculpted glutamate constitutive secretory pathway transport vesicle" EXACT [] GO:0060200 : clathrin sculpted acetylcholine transport vesicle + synonym: "clathrin sculpted acetylcholine constitutive secretory pathway transport vesicle" EXACT [] GO:0060201 : clathrin sculpted acetylcholine transport vesicle membrane + synonym: "clathrin sculpted acetylcholine constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0060202 : clathrin sculpted acetylcholine transport vesicle lumen + synonym: "clathrin sculpted acetylcholine constitutive secretory pathway transport vesicle lumen" EXACT [] GO:0060203 : clathrin sculpted glutamate transport vesicle membrane + synonym: "clathrin sculpted glutamate constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0060204 : clathrin sculpted glutamate transport vesicle lumen + synonym: "clathrin sculpted glutamate constitutive secretory pathway transport vesicle lumen" EXACT [] GO:0060640 : positive regulation of dentin-containing tooth bud formation by mesenchymal-epithelial signaling - name: positive regulation of dentine-containing tooth bud formation by mesenchymal-epithelial signaling + name: positive regulation of dentin-containing tooth bud formation by mesenchymal-epithelial signaling + synonym: "positive regulation of dentine-containing tooth bud formation by mesenchymal-epithelial signaling" RELATED [] GO:0060790 : tooth placode formation - def: The developmental process in which the tooth placode forms. An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud. + def: The developmental process in which the tooth placode forms. A tooth placode is a thickening of the ectoderm that will give rise to the tooth bud. GO:0061364 : apoptotic process involved in luteolysis - name: apoptosis involved in luteolysis + name: apoptotic process involved in luteolysis - def: The process of apoptosis that contributes to luteolysis. + def: The apoptotic process that contributes to luteolysis. + synonym: "apoptosis involved in luteolysis" NARROW [] + intersection_of: GO:0006915 + intersection_of: part_of GO:0001554 GO:0070081 : clathrin sculpted monoamine transport vesicle + synonym: "clathrin sculpted monoamine constitutive secretory pathway transport vesicle" EXACT [] GO:0070082 : clathrin sculpted monoamine transport vesicle lumen + synonym: "clathrin sculpted monoamine constitutive secretory pathway transport vesicle lumen" EXACT [] GO:0070083 : clathrin sculpted monoamine transport vesicle membrane + synonym: "clathrin sculpted monoamine constitutive secretory pathway transport vesicle membrane" EXACT [] GO:0070166 : enamel mineralization + relationship: part_of GO:0097186 GO:0070319 : Golgi to plasma membrane transport vesicle + synonym: "Golgi to plasma membrane constitutive secretory pathway transport vesicle" EXACT [] GO:0070381 : endosome to plasma membrane transport vesicle + synonym: "endosome to plasma membrane constitutive secretory pathway transport vesicle" EXACT [] GO:0070382 : exocytic vesicle + synonym: "exocytic constitutive secretory pathway transport vesicle" EXACT [] GO:0070468 : dentin secretion - name: dentine secretion + name: dentin secretion - def: The regulated release by odontoblasts of the extracellular matrix constituents, including collagen, that form the basis of dentine. + def: The regulated release by odontoblasts of the extracellular matrix constituents, including collagen, that form the basis of dentin. - synonym: "dentin secretion" EXACT [GOC:mah] + synonym: "dentine secretion" EXACT [GOC:mah] GO:0070538 : oleic acid binding - is_a: GO:0005504 + is_a: GO:0036041 GO:0070539 : linoleic acid binding - is_a: GO:0005504 + is_a: GO:0036041 GO:0070540 : stearic acid binding - is_a: GO:0005504 + is_a: GO:0036041 GO:0071895 : odontoblast differentiation - def: The process in which a relatively unspecialized cell of neural crest origin acquires the specialized features of an odontoblast, a cell on the outer surface of the dental pulp whose biological function is the creation of dentine. + def: The process in which a relatively unspecialized cell of neural crest origin acquires the specialized features of an odontoblast, a cell on the outer surface of the dental pulp whose biological function is the creation of dentin. GO:0090034 : regulation of chaperone-mediated protein complex assembly - name: regulation of cellular chaperone-mediated protein complex assembly + name: regulation of chaperone-mediated protein complex assembly - def: Any process that modulates the frequency, rate, or extent of cellular chaperone-mediated protein complex assembly. Cellular chaperone-mediated protein complex assembly is the aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell, mediated by chaperone molecules that do not form part of the finished complex. + def: Any process that modulates the frequency, rate, or extent of chaperone-mediated protein complex assembly. Chaperone-mediated protein complex assembly is the aggregation, arrangement and bonding together of a set of components to form a protein complex, mediated by chaperone molecules that do not form part of the finished complex. - intersection_of: regulates GO:0034619 + intersection_of: regulates GO:0051131 - relationship: regulates GO:0034619 + relationship: regulates GO:0051131 GO:0090035 : positive regulation of chaperone-mediated protein complex assembly - name: positive regulation of cellular chaperone-mediated protein complex assembly + name: positive regulation of chaperone-mediated protein complex assembly - def: Any process that increases the frequency, rate, or extent of cellular chaperone-mediated protein complex assembly. Cellular chaperone-mediated protein complex assembly is the aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell, mediated by chaperone molecules that do not form part of the finished complex. + def: Any process that increases the frequency, rate, or extent of chaperone-mediated protein complex assembly. Chaperone-mediated protein complex assembly is the aggregation, arrangement and bonding together of a set of components to form a protein complex, mediated by chaperone molecules that do not form part of the finished complex. - intersection_of: positively_regulates GO:0034619 + intersection_of: positively_regulates GO:0051131 - relationship: positively_regulates GO:0034619 + relationship: positively_regulates GO:0051131 GO:2001227 : quercitrin binding FILE STATS ========== Term counts for the old and new files Ontology Old file New file Change molecular function 9140 9148 +8 (9140 defined) (9148 defined) cellular component 2922 2924 +2 (2922 defined) (2924 defined) biological process 21591 21603 +12 (21591 defined) (21603 defined) Obsolete 1603 1603 0 (4.5% of total) (4.5% of total) (0.0%) Totals 33653 33675 +22 (+0.1%) 33653 (100.0%) defined 33675 (100.0%) defined 35256 inc. obs 35278 inc. obs