positive regulation of MBF transcription factor activity

[gocentral]

Ok, I just submitted these two term in TG freeform, ticked the box to get an email but didn't get it. Did it come through your end?

Label positive regulation of MBF transcription factor activity Definition Any process that activates or increases the frequency, rate or extent of activity of the transcription factor MBF. Xrefs PMID:11795845 Relations
is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity Meta-Data
namespace: biological_process subset: termgenie_unvetted created_by: TermGenie creation_date: 2014-01-29T14:43:44Z

ID: GO:1990278 Label: positive regulation of MBF transcription factor activity

2. Label negative regulation of MBF transcription factor activity Definition Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor MBF. Xrefs PMID:24006488 Relations
is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity Meta-Data
namespace: biological_process subset: termgenie_unvetted created_by: TermGenie creation_date: 2014-01-29T14:46:52Z

ID: GO:1990279 Label: negative regulation of MBF transcription factor activity

Reported by: antonialock

Original Ticket: geneontology/ontology-requests/10633

[gocentral]

Actually looking at this i wonder if I def did commit in my other SF ticket (the one about 7SK RNA)? Here, in the uncommited "please check this before submitting" bit it says Label positive regulation whereas after the go term has been generated it says Label: negative

there wasn't a colon in my notes to myself (in the other SF ticket)...

I still didn't get the email though!

Original comment by: antonialock

[gocentral]

I just emailed Heiko to point him to this SF ticket. Antonia's terms are indeed in the TG review page:

Details for commit #18603 User email a.lock@ucl.ac.uk Date 1/29/14 6:44 AM Commit MessageEdit Message TermGenie commit for user: al reviewed by pr No need to add IDs, they will be added to the commit message by TermGenie during commit. Term Hierarchy Generate Image Add Edit termMake Obsolete [Term] id: GO:1990278 name: positive regulation of MBF transcription factor activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of activity of the transcription factor MBF." [PMID:11795845] subset: termgenie_unvetted is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity created_by: al creation_date: 2014-01-29T14:43:44Z

and

Details for commit #18604 User email a.lock@ucl.ac.uk Date 1/29/14 6:47 AM Commit MessageEdit Message TermGenie commit for user: al reviewed by pr No need to add IDs, they will be added to the commit message by TermGenie during commit. Term Hierarchy Generate Image Add Edit termMake Obsolete [Term] id: GO:1990279 name: negative regulation of MBF transcription factor activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor MBF." [PMID:24006488] subset: termgenie_unvetted is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity created_by: al creation_date: 2014-01-29T14:46:52Z

Original comment by: paolaroncaglia

[gocentral]

From [go-discuss]

Pascale

Hello,

I thought there had been a decision a while ago not to create 'protein-specific' terms like this one, and to remove existing ones. Is this still the guideline ?

Thanks,

Pascale

Val

I agree, I'm guessing that the problem Antonia had was that MBF is a complex not a single gene product.

In this case Antonia, can we can do this instead?: GO:0001190 RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription
has_direct_substrate(MBF complex) (assuming this is one of the MBF binding regulators, then it could be an MF term) ?

Although:

1. Shouldn't this have the parent GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity ? The term GO:0001190 does not specify sequence specific, but there are sibling terms which refer to the core polymerase and the basal transcription machinery so I assume it is supposed to be the sequence-specific term ?

and

2. It is difficult for new curators to know when not to request these terms as there are lots of other "regulation of transcription factor x" for specific transcription factor terms in the ontology. We need to remove the precedent.

val

Rama

Val,

Yeap, using col-16 to indicate the MBF complex sounds good to me.

R

Original comment by: tberardini

[gocentral]

ok so do I put the CC in the extension then?

Original comment by: antonialock

[gocentral]

GO:0001190 RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription

This is a really clunky term name by the way....wouldn't it be much clearer if was called something like transcription factor activator (or similar?). I doubt many users would understand this term (I didn't until I thought hard at it and I probably have more patience than many biologists :) )

Original comment by: antonialock

[gocentral]

• status: open --> closed-works-for-me
• assigned_to: David Hill

Original comment by: ukemi

[gocentral]

Hi Antonia,

We needed to have a complex name like this because there are so many related 'transcription factor' terms that can be differentiates mechanistically, both by how they act mechanistically, the types of polymerase they work on and how they affect transcription. Just using a simple label like transcription factor would not represent these differences. When a user searches on 'transcription factor' they will get all these terms and then hopefully, just like you did, they will think about them to determine exactly what they mean.

I am going to close this item because the e-mail issue is being looked at and it seems like the annotation issue is being resolved.

-D

Original comment by: ukemi