Transcription jamboree: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(qu)
Line 22: Line 22:
==Discussion==
==Discussion==
* The reason we don't have a repressor term in MF is because the mechanism of 'how' it functions as a repressor is not clear in the literature. We should use the equivalent BP to represent this role.
* The reason we don't have a repressor term in MF is because the mechanism of 'how' it functions as a repressor is not clear in the literature. We should use the equivalent BP to represent this role.
*HERP1 could be annotated to 'corepressor binding', seq-specific DNA binding and the BP term
* HERP1 could be annotated to 'corepressor binding', seq-specific DNA binding and the BP term
*How can we have a term corepressor binding when we don't have a clear idea of what a repressor is. Both Midori and Karen felt that we don't need to have all the pieces defined for binding terms
* How can we have a term corepressor binding when we don't have a clear idea of what a repressor is. Both Midori and Karen felt that we don't need to have all the pieces defined for binding terms
*may be a composite term that describes these 3 pieces of evidence is appropriate
* May be a composite term that describes these 3 pieces of evidence is appropriate (Varsha/Karen)


= How much curator judgement is appropriate? =
= How much curator judgement is appropriate? =

Revision as of 16:53, 26 July 2011

Annotation Conf. Call, July 26, 2011

Examples for discussion at electronic Transcription Jamboree

Resources for curators

When do we have enough data for a MF annotation?

i) PMID 11486045 [VK] - Fig 2 - this data would have been previously annotated to the now obsolete term GO:0016564 transcription repressor activity.

- can we annotate to anything more than the biological process: 'GO:00045892; negative regulation of transcription, DNA-dependent', and 'DNA binding' as the molecular function?

- There is no indication anymore in the available MF terms of a proteins repressor activity, concerns about losing this information.

- if we can describe the binding of a protein as activating transcription in the molecular function ontology (GO 0001102 RNA polymerase II activating transcription factor binding ), why are we no longer able state that a transcription factor is activating or repressing in its activity?

Discussion

  • The reason we don't have a repressor term in MF is because the mechanism of 'how' it functions as a repressor is not clear in the literature. We should use the equivalent BP to represent this role.
  • HERP1 could be annotated to 'corepressor binding', seq-specific DNA binding and the BP term
  • How can we have a term corepressor binding when we don't have a clear idea of what a repressor is. Both Midori and Karen felt that we don't need to have all the pieces defined for binding terms
  • May be a composite term that describes these 3 pieces of evidence is appropriate (Varsha/Karen)

How much curator judgement is appropriate?

i) PMID 12270142 [VK] - as K/O of TWIST decreases expression of CBFA1, from figs 1 and 2 could we annotate to

GO:0045944 positive regulation of transcription from RNA polymerase II promoter

- More generally, if a curator is trying to describe the up-regulation of a protein-encoding gene, then is it correct to assume that regulation of expression would necessarily be via the RNA polymerase II. We shouldn't need direct evidence demonstrating the involvement of RNA polymerase II in the experiment?

- Similarly, based on fig 3 could we annotate to:

GO:2000679 positive regulation of transcription regulatory region DNA binding

Is this correct or are there other terms that should have been used instead?


- How can we support curators in judging the part of the DNA region that is being bound, e.g. so that curators can more easily identify a proximal region? Could we include in the curation manuals a diagram of the promoter/regulatory regions which bind proteins - and identify the protein that bind to distinct regions? (perhaps from Karen's presentation, linked to this page?)

- How do you know where an element is located - if the authors do not specifically state it is located upstream? For instance, in this case (PMID:19342457) the element is stated as NOT being upstream, but instead in an intron - how should we capture this data?

How do I annotate to one of the granular MF transcription factor activity terms when the evidence comes from 2 (or more) papers?

The gene CUP9 is described in the literature as a transcriptional repressor, but there is no single paper that contains evidence that allows annotation to the term that seems like the best description of its function. Note that these papers have a lot of information, but for this discussion, only short selections of each, indicated below, need to be looked at.

PMID:9427760 shows that:

  1. deletion of the CUP9 gene derepresses transcription of the PTR2 gene (Fig 2A and supporting text, right hand column of p 271 above the header). From this experiment, we can make the annotation negative regulation of transcription from RNA polymerase II promoter (GO:0000122) by IMP.
  2. CUP9 binds DNA (Fig 2B & brief discussion of figure on pp 271-2 under the heading "Cup9p is a repressor of the PTR2 gene"). From this experiment, we can make the annotation: RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978) by IDA

PMID:18708352 shows that CUP9 interacts with CYC8(SSN6)/TUP1 (Fig 2B and text beginning with "To address this experimentally, we carried out a coimmunoprecipitation assay, using epitope-tagged SSN6 and CUP9 (Fig. 2B).". From this, we can make the annotation RNA polymerase II repressing transcription factor binding (GO:0001103) by IPI with CYC8 (aka SSN6).

Using these pieces of evidence in combination, the term sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133) would be a good description of the overall activity of Cup9, but since neither these papers, or any others available for CUP9, show all the evidence for this term in a single paper, how do you annotate to a term like this?

How do I find the correct transcription factor activity from these terms

GO:0000982 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity

Definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.

and GO:0001133 sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity

Definition: Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II.

They sound the same but they are not even parent/child (Not that the only annotation to the second term is S. cerevisiae GAL4 IC only CUP9 IC only SFL1 IPI only)

See QuickGO ancestor chart view here: http://www.ebi.ac.uk/QuickGO/GMultiTerm#a=64%2400FM00Hj&c&tab=chart

Original SourceForge request here: https://sourceforge.net/tracker/?func=detail&aid=3377031&group_id=36855&atid=440764