transcription factor AP-1 complex

gocentral commented 14 years ago

Hi

please create the following 2 related terms

Process term GO:0051091 positive regulation of transcription factor activity > Is a child new term: positive regulation of transcription factor AP1 complex activity With ref: dbxrf: BHF Definition: Any process that activates or increases the frequency, rate or extent of activity of the AP1 transcription factor complex. AP1 transcription factor complex is composed of heterodimers of the Jun and Fos family proteins. Exact synonym: positive regulation of transcription factor AP-1 complex activity Exact synonym: positive regulation of transcription factor activating protein 1 complex activity
Component term GO:0005667 transcription factor complex > is a child new term: transcription factor AP1 complex Definition: a dimeric transcription factor complex composed of proteins from several families whose common denominator is the possession of basic leucine zipper (bZIP) domains that are essential for dimerization and DNA binding. The major subfamilies are Fos or Jun (c-Jun, JunB, JunD; c-Fos, FosB, Fra-1, Fra-2) but additional subfamilies include activating transcription factor (ATF) proteins (ATF2, LRF1/ATF3, B-ATF, JDP1, JDP2) and Maf (c-Maf, MafB, MafA, MafG/F/K, Nrl). Jun-Fos heterodimers bind preferentially to a heptamer consensus sequence, TPA responsive element (TRE), whereas Jun-ATF dimers bind the cyclic AMP responsive element (CRE). Exact synonym: transcription factor AP-1 complex Exact synonym: transcription factor activating protein 1 complex from PMID: 20060892 review

With ref: dbxrf: BHF

For the annotation of PMID: 12296995 RANK/TNFRSF11A Q9Y6Q6 and TRAF2, 5, 6 Q12933, O00463, Q9Y4K3

Thanks

Ruth

Reported by: RLovering

Original Ticket: geneontology/ontology-requests/7560

gocentral commented 14 years ago

assigned_to: nobody --> ukemi

Original comment by: mah11

gocentral commented 14 years ago

assigned_to: ukemi --> kchris

Original comment by: ukemi

gocentral commented 14 years ago

Hi Ruth,

Regarding the process term, I do not think we should add this. I hadn't looked at children of "positive regulation of transcription factor activity" or of its "negative regulation ..." sibling, before. I just hadn't really spend much time looking at the regulation terms. Below is the current list of existing children of these terms:

GO:0051090 - regulation of transcription factor activity

GO:0051091 - positive regulation of transcription factor activity -- GO:0051092 - positive regulation of NF-kappaB transcription factor activity --- GO:0006985 - positive regulation of NF-kappaB transcription factor activity by ER overload response -- GO:0032793 - positive regulation of CREB transcription factor activity -- GO:0007228 - positive regulation of hh target transcription factor activity
GO:0043433 - negative regulation of transcription factor activity -- GO:0032792 - negative regulation of CREB transcription factor activity -- GO:0032088 - negative regulation of NF-kappaB transcription factor activity

but now that I have, I think that these terms should be obsoleted for the same reason we have already agreed to obsolete the child terms or "transcription factor binding" and of "promoter binding" that refer to specific transcription factors or to specific DNA motifs.

So, I think that we should keep the top level term (GO:0051091 - positive regulation of transcription factor activity) and that those who wish to capture regulation of -which- transcription factor will need to use column 16.

For the most detailed term (GO:0006985 - positive regulation of NF-kappaB transcription factor activity by ER overload response), I would be inclined to make a new term for this type of regulation, but not specific to this specific transcription factor, so I think we could have a term for "positive regulation of transcription factor activity by ER overload response", so that we can represent this mode of regulation, but in a way that can be used for any transcription factor that might be regulated in this way.

Regarding the component term, that's fine. I'll add it. Unless and until there's a decision that this level of detail belongs in another ontology, such as PRO, we need them in GO so that you have a way to refer to the complex in column 16 for other annotations.

-Karen

Original comment by: krchristie