Transcription factor related

[gocentral]

This is related to the 'TF related' 14573 on the annotation tracker.

Basically I am trying to get all of my general and seqeunce specific TFs separated by function term, (ignoring for the moment whether these are bona fida functions...I currently have one foot in both camps!)

Anyway I think now I maybe should have been using

specific RNA polymerase II transcription factor activity and general ....

So probably the new terms M. suggested in 14573 already exist

Should 'specific RNA polymerase II transcription factor activity' and 'general...' have the parent transcription factor activity? currently they don't which is why it took me a while to locate them...

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/3154":https://sourceforge.net/p/geneontology/ontology-requests/3154

[gocentral]

Logged In: YES user_id=516865

and should these also have DNA binding as a parent.

THese are the gene products i am trying to group. Sequence specific DNA binding transcription factors.....

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=473890

Hi,

I'm not sure that the "general RNA polymerase II transcription factor activity" term should have parent under the term "transcription factor activity" because the current term has parentage under "DNA binding" and I'm not sure that all of the general transcription factors have DNA binding activity. It's
possible that some may bind to another factor or the polymerase, but not to DNA directly. I'll have to check, or maybe I could just send an email to my PhD advisor. Unfortunately, the def doesn't really seem to clarify what the term is intended for. The current def of:

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.

seems about as broad as the def for one of its parent terms:

transcription regulator activity: Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.

Did this definition ever get updated after the January 2004 GO meeting in which transcription factor was such a contentious issue?

-Karen

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=554670

Huh... We did have a big discussion about this definition. I posted the concensus definition a while back and it looks like it has disappeared?

Here's the URL for the previous item

http://sourceforge.net/tracker/index.php?func=detail&aid=1114890&group\_id=36855&atid=440764

Original comment by: eurie

[gocentral]

Logged In: YES user_id=516865

Hi Karen, you are probably correct that

"general RNA polymerase II transcription factor activity" should not have the parent "transcription factor activity" which is good wbecasue it means that I didn't make Sandra remove the Interpro mappings unnecisarily.

This would work for me as all of my 'specific sequence binding transcription factors' would be annotated to this term, and my general transcription factors wouldn't be. I am trying to make it possible to retreive these two sets seperately based on their function annotation.

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=516865

As a follow up to this....

As this term excludes general transcription factors, perhaps we could rename "transcription factor activity" to "regulatory transcription factor" syn rTF and mak transcription factor activity a synonym.

I think this would be more in keeping with the current def of

Original comment by: ValWood

[gocentral]

• summary: TFreanscription factor related --> Transcription factor related

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=473890

I think calling this term 'regulatory transcription factor activity' would be a great idea. Shortly after the confrontational 2003 GO meeting at Stanford, I went surfing around some web sites put up by transcription people. There was one by Steve Buratowski that used exactly that phrase, though I should point out that I can't find that site right now...

Anyway, I think this name makes it clearer what we are binning into this group.

-Karen

Original comment by: krchristie

[gocentral]

• assigned_to: nobody --> kchris

Original comment by: mah11

[gocentral]

Logged In: YES user_id=473890 Originator: NO

consolidating this item into this previous one:

[ 704985 ] transcription factor activity https://sourceforge.net/tracker/index.php?func=detail&aid=704985&group\_id=36855&atid=440764

Original comment by: krchristie

[gocentral]

• status: open --> closed-duplicate

Original comment by: krchristie

[gocentral]

• milestone: --> PomBase

Original comment by: mah11