search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
220 stars 40 forks source link

are SMAD complexes nucleocytoplasmic shuttling complexes? #11626

Closed gocentral closed 9 years ago

gocentral commented 9 years ago

Hi,

SMAD2 and SMAD3 get phosphorylated at the TGFbeta receptors, form heterotetramers with SMAD4 and move to the nucleus where they act as transcription factors (in a nutshell!).

Can they have

GO:0031074 nucleocytoplasmic shuttling complex def: Any complex that acts to move proteins or RNAs into or out of the nucleus through nuclear pores.

as an is_a parent? I'm not sure if this term only refers to complexes that move other proteins or RNAs that subsequently get 'unloaded'.

If yes to the above, should they have logical extensions to GO:0006913 nucleocytoplasmic transport and GO:0005487 nucleocytoplasmic transporter activity?

In any case, I think the heteromeric SMAD complexes

GO:0071144 SMAD2-SMAD3 protein complex GO:0071145 SMAD2-SMAD4 protein complex GO:0071146 SMAD3-SMAD4 protein complex

should have GO:0005667 transcription factor complex as is_a parent.

Birgit

Reported by: bmeldal

Original Ticket: geneontology/ontology-requests/11455

gocentral commented 9 years ago

Don't think so. This term is for complexes that function in transport of other proteins and RNAs through the nuclear pore, not for the transported complexes.

Original comment by: dosumis

gocentral commented 9 years ago

Original comment by: dosumis

gocentral commented 9 years ago

I thought I'd check but that was what I thought the nucleocytoplasmic shuttling terms were for.

Is the GO:0005667 transcription factor complex parentage ok though?

Birgit

Original comment by: bmeldal

gocentral commented 9 years ago

Is the GO:0005667 transcription factor complex parentage ok though?

Yep. Have added this by specifying function.

capable_of 'sequence-specific DNA binding transcription factor activity'

Original comment by: dosumis

gocentral commented 9 years ago

Original comment by: dosumis

gocentral commented 9 years ago

Thanks :)

Original comment by: bmeldal

gocentral commented 9 years ago

GO:0005667 transcription factor doesn't show up yet as a parent in QuickGo.

Original comment by: bmeldal

gocentral commented 9 years ago

It's in the public release of GO. So presumably just QuickGO being slow to update.

Original comment by: dosumis

gocentral commented 9 years ago

Ok, will check again next week. Although 'slow' is an understatement as you made the changes >1 week ago...

Original comment by: bmeldal