Gene Ontology Ontology Comparison Report ========================== Files used: - file 1 (old): go-2011-12-31.obo; date: 23:12:2011 10:41; CVS revision: 1.2470 - file 2 (new): go-2012-01-07.obo; date: 06:01:2012 16:33; CVS revision: 1.2481 NEW TERMS ========= ID name namespace GO:0036086 positive regulation of transcription from RNA polymerase II promoter in response to iron ion starvation biological_process GO:0036087 glutathione synthase complex cellular_component GO:0036088 D-serine catabolic process biological_process GO:0038057 TNFSF11 binding molecular_function GO:0038058 TNFSF11 receptor activity molecular_function GO:0039531 regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway biological_process GO:0039532 negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway biological_process GO:0039533 regulation of MDA-5 signaling pathway biological_process GO:0039534 negative regulation of MDA-5 signaling pathway biological_process GO:0039535 regulation of RIG-I signaling pathway biological_process GO:0039536 negative regulation of RIG-I signaling pathway biological_process GO:0039537 suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway biological_process GO:0039538 suppression by virus of host RIG-I signaling pathway biological_process GO:0039539 suppression by virus of host MDA-5 signaling pathway biological_process GO:0097205 renal filtration biological_process GO:0097206 nephrocyte filtration biological_process GO:0097207 bud dormancy process biological_process GO:0097208 alveolar lamellar body cellular_component GO:0097209 epidermal lamellar body cellular_component OBSOLETIONS =========== None TERM MERGES =========== GO:0007513, pericardial cell differentiation was merged into GO:0061320, pericardial nephrocyte differentiation GO:0007514, garland cell differentiation was merged into GO:0061321, garland nephrocyte differentiation TERM CHANGES ============ GO:0003094 : glomerular filtration - is_a: GO:0003014 + is_a: GO:0097205 GO:0003381 : epithelial cell morphogenesis involved in gastrulation - is_a: GO:0007369 + relationship: part_of GO:0007369 GO:0004430 : 1-phosphatidylinositol 4-kinase activity - is_a: GO:0001727 GO:0004438 : phosphatidylinositol-3-phosphatase activity - is_a: GO:0042577 GO:0007249 : I-kappaB kinase/NF-kappaB cascade - def: A series of reactions initiated by the activation of the transcription factor NF-kappaB. NF-kappaB is sequestered by the inhibitor I-kappaB, and is released when I-kappaB is phosphorylated by activated I-kappaB kinase. + def: The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of IKK and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. - synonym: "NF-kappaB cascade" EXACT [] - synonym: "NIK-I-kappaB/NF-kappaB cascade" EXACT [] + synonym: "canonical NF-kappaB signaling cascade" EXACT [GOC:bf] + synonym: "p50-dependent NF-kappaB signaling" RELATED [PMID:18292232] + synonym: "NF-kappaB cascade" BROAD [] + xref: REACTOME:REACT_13696.1 "NF-kB is activated and signals survival, Homo sapiens" GO:0007250 : activation of NF-kappaB-inducing kinase activity - relationship: part_of GO:0007249 GO:0007252 : I-kappaB phosphorylation - def: The process of introducing a phosphate group into an I-kappaB protein. + def: The process of introducing a phosphate group into an inhibitor of kappa B (I-kappaB) protein. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing bound NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. + synonym: "IKB phosphorylation" EXACT [GOC:bf] + synonym: "IkappaB phosphorylation" EXACT [GOC:bf] + synonym: "inhibitor of NF-kappaB phosphorylation" EXACT [GOC:bf] + synonym: "inhibitor of kappaB phosphorylation" EXACT [GOC:bf] GO:0007253 : cytoplasmic sequestering of NF-kappaB - relationship: part_of GO:0007249 + relationship: part_of GO:0043124 GO:0007263 : nitric oxide mediated signal transduction - def: A series of molecular signals mediated by the detection of nitric oxide (NO). + def: A series of molecular signals mediated by nitric oxide (NO). GO:0008384 : IkappaB kinase activity - comment: Note that phosphorylation of IkappaB targets it for proteasomal degradation and allows the nuclear translocation of kB. The kinase is composed of alpha, beta and gamma subunits, of which the latter does not have kinase activity but is presumed to play a regulatory role. + comment: Note that phosphorylation of IkappaB targets it for proteasomal degradation and allows the nuclear translocation of kB. + relationship: part_of GO:0007252 GO:0008385 : IkappaB kinase complex - def: A protein serine/threonine kinase that phosphorylates IkappaB, thereby targeting this for proteasomal degradation and allowing the nuclear translocation of kB. Composed of alpha, beta and gamma subunits, the latter not having kinase activity but presumed to play a regulatory role. + def: A trimeric protein complex that phosphorylates inhibitory-kappaB (I-kappaB) proteins. The complex is composed of two kinase subunits (alpha and beta) and a regulatory gamma subunit (also called NEMO). In a resting state, NF-kappaB dimers are bound to inhibitory IKB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. GO:0008588 : release of cytoplasmic sequestered NF-kappaB + relationship: negatively_regulates GO:0007253 GO:0009740 : gibberellic acid mediated signaling pathway - is_a: GO:0071370 GO:0009753 : response to jasmonic acid stimulus - is_a: GO:0009719 - is_a: GO:0010033 + is_a: GO:0009725 GO:0009867 : jasmonic acid mediated signaling pathway + synonym: "jasmonate signaling" RELATED [PMID:16478936] + synonym: "JA signaling" EXACT [PMID:20159850] - is_a: GO:0007165 + is_a: GO:0009755 GO:0010162 : seed dormancy process - name: seed dormancy + name: seed dormancy process - def: The process in which a dormant state is induced, maintained and broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated. + def: A dormancy process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a seed. Seed dormancy is a suspension of most physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leaching of inhibitors. + synonym: "seed dormancy" RELATED [] GO:0010476 : gibberellin mediated signaling pathway + is_a: GO:0071370 GO:0016303 : 1-phosphatidylinositol-3-kinase activity - is_a: GO:0035004 + is_a: GO:0052742 GO:0016307 : phosphatidylinositol phosphate kinase activity - is_a: GO:0001727 GO:0016314 : phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity - is_a: GO:0042577 GO:0016316 : phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity - is_a: GO:0042577 GO:0022002 : negative regulation of anterior neural cell fate commitment of the neural plate by Wnt receptor signaling pathway - intersection_of: GO:0016055 - intersection_of: part_of GO:0022001 GO:0022003 : negative regulation of anterior neural cell fate commitment of the neural plate by fibroblast growth factor receptor signaling pathway - intersection_of: GO:0008543 - intersection_of: part_of GO:0022001 GO:0022611 : dormancy process - def: The process in which a dormant state is induced, maintained or broken. Dormancy is characterized by a suspension of physiological activity. + def: A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. + comment: In plants and animals, dormancy may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. In plants, dormancy may involve the formation of dormant buds, and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system in herbaceous perennials. The exit from dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium. + synonym: "multicellular organism dormancy process" NARROW [] GO:0032958 : inositol phosphate biosynthetic process - comment: See also the biological process term 'inositol or phosphatidylinositol phosphorylation ; GO:0046853'. GO:0033217 : regulation of transcription from RNA polymerase II promoter in response to iron ion starvation - def: Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of iron ions. + def: Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions. GO:0033256 : I-kappaB/NF-kappaB complex - def: A protein complex containing an I-kappaB protein and one or more copies of an NF-kappaB protein; mediates regulation of NF-kappaB activity by I-kappaB. + def: A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. GO:0033885 : lipid-phosphate phosphatase activity - synonym: "(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphohydrolase activity" EXACT [EC:3.1.3.76] - synonym: "dihydroxy fatty acid phosphatase activity" EXACT [EC:3.1.3.76] - synonym: "hydroxy lipid phosphatase activity" EXACT [EC:3.1.3.76] - synonym: "hydroxy fatty acid phosphatase activity" EXACT [EC:3.1.3.76] + synonym: "hydroxy lipid phosphatase activity" BROAD [EC:3.1.3.76] + synonym: "hydroxy fatty acid phosphatase activity" BROAD [EC:3.1.3.76] + synonym: "(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity" EXACT [EC:3.1.3.76] + synonym: "(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphohydrolase activity" EXACT systematic_synonym [EC:3.1.3.76] + synonym: "dihydroxy fatty acid phosphatase activity" BROAD [EC:3.1.3.76] GO:0034597 : phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity - is_a: GO:0042577 GO:0035004 : phosphatidylinositol 3-kinase activity - is_a: GO:0016773 - is_a: GO:0052742 - is_a: GO:0001727 + is_a: GO:0016301 GO:0035005 : 1-phosphatidylinositol-4-phosphate 3-kinase activity - is_a: GO:0035004 GO:0039528 : cytoplasmic pattern recognition receptor signaling pathway in response to virus + synonym: "virus-induced cytoplasmic pattern recognition receptor signaling pathway" EXACT [GOC:bf] GO:0042348 : NF-kappaB import into nucleus + synonym: "NF-KB import into nucleus" EXACT [GOC:bf] + relationship: part_of GO:0007249 GO:0042599 : lamellar body - def: A membrane-bounded organelle, specialized for the storage and secretion various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome. + def: A membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome. - synonym: "keratinosome" EXACT [] - synonym: "Odland body" EXACT [] + synonym: "keratinosome" NARROW [] + synonym: "Odland body" NARROW [] GO:0042751 : estivation + synonym: "aestivation" EXACT [GOC:pr] GO:0042770 : signal transduction in response to DNA damage - intersection_of: GO:0007165 - intersection_of: part_of GO:0006974 GO:0046746 : virus budding from nuclear membrane by viral capsid re-envelopment - intersection_of: GO:0046765 - intersection_of: part_of GO:0046745 GO:0046747 : virus budding from Golgi membrane by viral capsid re-envelopment - intersection_of: GO:0046763 - intersection_of: part_of GO:0046745 GO:0046748 : virus budding from ER membrane by viral capsid re-envelopment - intersection_of: GO:0046764 - intersection_of: part_of GO:0046745 GO:0046749 : virus budding from nuclear membrane by viral capsid envelopment - intersection_of: GO:0046765 - intersection_of: part_of GO:0046744 GO:0046750 : virus budding from Golgi membrane by viral capsid envelopment - intersection_of: GO:0046763 - intersection_of: part_of GO:0046744 GO:0046751 : virus budding from ER membrane by viral capsid envelopment - intersection_of: GO:0046764 - intersection_of: part_of GO:0046744 GO:0046767 : virus budding from plasma membrane by viral capsid envelopment - intersection_of: GO:0046766 - intersection_of: part_of GO:0046744 GO:0046768 : virus budding from plasma membrane by viral capsid re-envelopment - intersection_of: GO:0046766 - intersection_of: part_of GO:0046745 GO:0050977 : magnetoreception by sensory perception of chemical stimulus - intersection_of: GO:0007606 - intersection_of: part_of GO:0050958 GO:0050978 : magnetoreception by sensory perception of electrical stimulus - intersection_of: GO:0050952 - intersection_of: part_of GO:0050958 GO:0051800 : phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity - is_a: GO:0042577 GO:0052482 : defense response by cell wall thickening - intersection_of: GO:0052386 - intersection_of: part_of GO:0006952 GO:0052542 : defense response by callose deposition - intersection_of: GO:0052545 - intersection_of: part_of GO:0006952 GO:0052742 : phosphatidylinositol kinase activity + is_a: GO:0016773 GO:0052813 : phosphatidylinositol bisphosphate kinase activity + is_a: GO:0016773 GO:0060852 : regulation of transcription involved in venous endothelial cell fate commitment - is_a: GO:0060845 + relationship: part_of GO:0060845 GO:0061006 : regulation of cell proliferation involved in kidney morphogenesis - is_a: GO:0060993 + relationship: part_of GO:0060993 GO:0061320 : pericardial nephrocyte differentiation + alt_id: GO:0007513 + synonym: "pericardial cell differentiation" NARROW [] + is_a: GO:0035051 GO:0061321 : garland nephrocyte differentiation + alt_id: GO:0007514 + synonym: "garland cell differentiation" EXACT [] + relationship: part_of GO:0001700 GO:0070178 : D-serine metabolic process + is_a: GO:0046416 GO:0070335 : aspartate binding - def: Interacting selectively and non-covalently with glutamate, the anion of 2-aminobutanedioic acid. + def: Interacting selectively and non-covalently with aspartate, the alpha-amino-acid anion of 2-aminobutanedioic acid that has formula C4H5NO4. GO:0071395 : cellular response to jasmonic acid stimulus - is_a: GO:0071310 - is_a: GO:0071495 + is_a: GO:0032870 GO:0071847 : TNFSF11-mediated signaling pathway - def: A series of molecular signals generated as a consequence of TNFSF11 binding to a cell surface receptor. + def: A series of molecular signals generated as a consequence of tumor necrosis factor ligand superfamily member 11 (TNFSF11) binding to a cell surface receptor. GO:0072535 : tumor necrosis factor (ligand) superfamily member 11 production - synonym: "TNFSF11 production" EXACT [GOC:mah] - synonym: "RANKL production" EXACT [GOC:ebc] + synonym: "TNFSF11 production" EXACT [GOC:mah, PRO:000002107] + synonym: "tumor necrosis factor ligand superfamily member 11 production" EXACT [GOC:bf, PR:000002107] + synonym: "RANKL production" EXACT [GOC:ebc, PR:000002107] GO:0090375 : negative regulation of transcription from RNA polymerase II promoter in response to iron ion starvation - def: Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of iron ions. + def: Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions. + is_a: GO:0097201 GO:0097201 : negative regulation of transcription from RNA polymerase II promoter in response to stress + is_a: GO:0000122 GO:2000033 : regulation of seed dormancy process - name: regulation of seed dormancy + name: regulation of seed dormancy process - def: Any process that modulates the frequency, rate or extent of seed dormancy. + def: Any process that modulates the frequency, rate or extent of seed dormancy process. + synonym: "regulation of seed dormancy" RELATED [] FILE STATS ========== Term counts for the old and new files Ontology Old file New file Change molecular function 9203 9205 +2 (9203 defined) (9205 defined) cellular component 2941 2944 +3 (2941 defined) (2944 defined) biological process 21753 21765 +12 (21753 defined) (21765 defined) Obsolete 1609 1609 0 (4.5% of total) (4.5% of total) (0.0%) Totals 33897 33914 +17 (0.0%) 33897 (100.0%) defined 33914 (100.0%) defined 35506 inc. obs 35523 inc. obs