TF related

[gocentral]

I am working wih Tony Wright at the Karolinska to try to refine and extend the list of S. pombe regulatory transcription factors in pombe, ie ones that we expect to bind to specific DNA sequences.

So in Go we have:

GO:0003700 transcription factor activity Any activity required to initiate or regulate transcription; includes the actions of both gene regulatory proteins as well as the general transcription factors.

Many Interpro mappings have been made to this term, which seems perfectly reasonable based on its current def.

However, by this term, do we mean the transcription 'factors' which are part of the general RNA pol I/II and III machinery, I didn't think we did becasue a) these have their own terms, and b) these are not 'real' function terms but function grouping terms for 'factors' known to be members of RNA polymerase I II and III complexes and subcomplexes. i.e. they are process terms in function which will each have specific functions

This may be completely wrong, if so please correct me!

In light of the above (if it is correct), here are some suggested updated mapping to remove the 'transcription factor activity' from things which are not 'transcription factors which bind specific DNA sequences' (if this is what it means)

IPR000812 is present in TFIIB &TFIIC so this probably needs to go to the parent transcription regulator activity GO:0030528 ?

IPR001222 not sure abut this as it isn't specific for 'transcription factor activity' is also in RNA polymerase subunits rpa12/O94703 rpb9/O74635 and rpc11/O13896and in tfs1/P49373

IPR007309 GO:0003709 : RNA polymerase III transcription factor activity `

IPR007198 GO:0003702 : RNA polymerase II transcription factor activity

IPR003923 GO:0003702 : RNA polymerase II transcription factor activity

IPR006809 GO:0003702 : RNA polymerase II transcription factor activity

IPR011442 wasn't sure here/ both? GO:0016986 transcription initiation factor activity GO:0003702 : RNA polymerase II transcription factor activity

IPR004598 Transcription factor Tfb2 would probably be better renamed Transcription factor TFIIH subunit Tfb2 GO:0003702 : RNA polymerase II transcription factor activity

IPR004600
Transcription factor Tfb4 would probably be better renamed Transcription factor TFIIH subunit Tfb4 GO:0003702 : RNA polymerase II transcription factor activity

IPR006289 GO:0003702 : RNA polymerase II transcription factor activity and/or GO:0003746 translation elongation factor activity

I think these are correct, but Sandra you'll probably spot if I have made them too specific...some could probably be more specific like 'general RNA polymerase II transcription factor activity'

Val

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/203":https://sourceforge.net/p/geneontology/annotation-issues/203

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one more IPR006751 GO:0003702 : RNA polymerase II transcription factor

Original comment by: ValWood

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• milestone: --> InterPro

Original comment by: mah11

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There is a camp that regards the terms 'transcription regulator activity' and most, if not all, of its children as process terms in disguise (privately, my sympathies lie with that camp). given that we're stuck with them ...

> do we mean the transcription 'factors' which are > part of the general RNA pol I/II and III machinery

I think so ... I suppose there ought to be 'general' and 'specific' TF activity terms under the parent 'transcription factor activity', mirroring the children of RNAPII TF activity; I've never got round to putting them in, and neither has anyone else...

m

Original comment by: mah11

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Original comment by: mah11

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In this case this would make all of these mappings correct, as these terms would become children of general (the terms I have suggested would then just be more granular).

I could then use the term 'specific transcription factor activity for all the ones I would like to separate out'

however, i came across another which probably does want fixing. IPR001789 is mapped to DNA binding and I'm not sure that this is the DNA binding domain.

Also should the def of transcription factor activity mention DNA binding (it is a parent but)

Original comment by: ValWood

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I have corrected IPR001789, I agree that was not the DNA binding domain.

IPR000812 is present in TFIIB &TFIIC so this probably needs to go to the parent transcription regulator activity GO:0030528 ?

Done

IPR001222 not sure abut this as it isn't specific for 'transcription factor activity' is also in RNA polymerase subunits rpa12/O94703 rpb9/O74635 and rpc11/O13896and in tfs1/P49373

I've moved it up to "Transcriptional regulator" - I couldn't see anything more appropriate

IPR007309 GO:0003709 : RNA polymerase III transcription factor activity ` OK, in that it encompasses regulation.

IPR007198 GO:0003702 : RNA polymerase II transcription factor activity Done - and Zn binding also added

IPR003923 GO:0003702 : RNA polymerase II transcription factor activity Done

IPR006809 GO:0003702 : RNA polymerase II transcription factor activity Done

IPR011442 wasn't sure here/ both? GO:0016986 transcription initiation factor activity GO:0003702 : RNA polymerase II transcription factor activity

I think both look good.

IPR004598 Transcription factor Tfb2 would probably be better renamed Transcription factor TFIIH subunit Tfb2 GO:0003702 : RNA polymerase II transcription factor activity

IPR004600 Transcription factor Tfb4 would probably be better renamed Transcription factor TFIIH subunit Tfb4 GO:0003702 : RNA polymerase II transcription factor activity Done - I'm passing the renaming suggestions on to Louise Daugherty who is responsible for that particular can of worms.

IPR006289 GO:0003702 : RNA polymerase II transcription factor activity and/or GO:0003746 translation elongation factor activity Again both look relevant.

Sandra

Original comment by: orchard

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Original comment by: orchard

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Hi Sandra,

It is possible that some of these were OK, and that they should alredy be children of transcription factor activity.

Anyway, when my GO editoiral query related to this is resolved I'll go through these and let you know if there are any better mappings. In the meantime, none of these are incorrect.

Thanks

Val

Original comment by: ValWood