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

Obsoletions

None

Term merges

Old ID Old name Merged into Merged term name
GO:0007513pericardial cell differentiationGO:0061320pericardial nephrocyte differentiation
GO:0007514garland cell differentiationGO:0061321garland nephrocyte differentiation

Term changes

Changes in term-related data
File 1 (23:12:2011 10:41, 1.2470) File 2 (06:01:2012 16:33, 1.2481)
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.
synonym
"NF-kappaB cascade" EXACT []
"NIK-I-kappaB/NF-kappaB cascade" EXACT []
 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
"canonical NF-kappaB signaling cascade" EXACT [GOC:bf]
"NF-kappaB cascade" BROAD []
"p50-dependent NF-kappaB signaling" RELATED [PMID:18292232]
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
"IkappaB phosphorylation" EXACT [GOC:bf]
"IKB phosphorylation" EXACT [GOC:bf]
"inhibitor of kappaB phosphorylation" EXACT [GOC:bf]
"inhibitor of NF-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
GO:0010033
 is_a
GO:0009725
GO:0009867 : jasmonic acid mediated signaling pathway
is_a
GO:0007165
 synonym
"JA signaling" EXACT [PMID:20159850]
"jasmonate signaling" RELATED [PMID:16478936]
is_a
GO:0009755
GO:0010162 : seed dormancy process
name
seed dormancy
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.
 name
seed dormancy process
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
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
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]
"dihydroxy fatty acid phosphatase activity" EXACT [EC:3.1.3.76]
"hydroxy fatty acid phosphatase activity" EXACT [EC:3.1.3.76]
"hydroxy lipid phosphatase activity" EXACT [EC:3.1.3.76]
 synonym
"(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity" EXACT [EC:3.1.3.76]
"(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphohydrolase activity" EXACT systematic_synonym [EC:3.1.3.76]
"dihydroxy fatty acid phosphatase activity" BROAD [EC:3.1.3.76]
"hydroxy fatty acid phosphatase activity" BROAD [EC:3.1.3.76]
"hydroxy lipid 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:0001727
GO:0016773
GO:0052742
 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.
synonym
"keratinosome" EXACT []
"Odland body" EXACT []
 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" NARROW []
"Odland body" NARROW []
GO:0042751 : estivation
synonym
"aestivation" EXACT [GOC:pr]
GO:0042770 : signal transduction in response to DNA damage
intersection_of
GO:0007165
part_of GO:0006974
GO:0046746 : virus budding from nuclear membrane by viral capsid re-envelopment
intersection_of
GO:0046765
part_of GO:0046745
GO:0046747 : virus budding from Golgi membrane by viral capsid re-envelopment
intersection_of
GO:0046763
part_of GO:0046745
GO:0046748 : virus budding from ER membrane by viral capsid re-envelopment
intersection_of
GO:0046764
part_of GO:0046745
GO:0046749 : virus budding from nuclear membrane by viral capsid envelopment
intersection_of
GO:0046765
part_of GO:0046744
GO:0046750 : virus budding from Golgi membrane by viral capsid envelopment
intersection_of
GO:0046763
part_of GO:0046744
GO:0046751 : virus budding from ER membrane by viral capsid envelopment
intersection_of
GO:0046764
part_of GO:0046744
GO:0046767 : virus budding from plasma membrane by viral capsid envelopment
intersection_of
GO:0046766
part_of GO:0046744
GO:0046768 : virus budding from plasma membrane by viral capsid re-envelopment
intersection_of
GO:0046766
part_of GO:0046745
GO:0050977 : magnetoreception by sensory perception of chemical stimulus
intersection_of
GO:0007606
part_of GO:0050958
GO:0050978 : magnetoreception by sensory perception of electrical stimulus
intersection_of
GO:0050952
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
part_of GO:0006952
GO:0052542 : defense response by callose deposition
intersection_of
GO:0052545
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
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
"RANKL production" EXACT [GOC:ebc]
"TNFSF11 production" EXACT [GOC:mah]
 synonym
"RANKL production" EXACT [GOC:ebc, PR:000002107]
"TNFSF11 production" EXACT [GOC:mah, PRO:000002107]
"tumor necrosis factor ligand superfamily member 11 production" EXACT [GOC:bf, 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
def
Any process that modulates the frequency, rate or extent of seed dormancy.
 name
regulation of seed dormancy process
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
9203 (100.0%) defined 		9205
9205 (100.0%) defined 		+2
cellular component 2941
2941 (100.0%) defined 		2944
2944 (100.0%) defined 		+3
biological process 21753
21753 (100.0%) defined 		21765
21765 (100.0%) defined 		+12
Obsolete 1609
(4.5% of total)		 1609
(4.5% of total)		 0 (0.0%)
Totals 33897
33897 (100.0%) defined
35506 inc. obsoletes 		33914
33914 (100.0%) defined
35523 inc. obsoletes 		+17 (0.0%)

Ontology report info