20101108 AnnotationCallMinutes

From GO Wiki
Revision as of 14:37, 10 November 2010 by Rama (talk | contribs) (PMID 8655543 (GLN3 paper))

Jump to: navigation, search

Annotation Jamboree

The Annotation conference call for November will feature an annotation jamboree.
The call is scheduled for Nov 8, 2010 (Monday) at 8:00 AM California time.

We will try a new format this time. We have picked 2 papers on transcription for this jamboree (yes, they are yeast papers!).
1) PMID 7568152
Role of the GATA factors Gln3p and Nil1p of Saccharomyces cerevisiae in the expression of nitrogen-regulated genes. Stanbrough M, Rowen DW, Magasanik B.
2) PMID 8655543
G1n3p is capable of binding to UAS(NTR) elements and activating transcription in Saccharomyces cerevisiae. Cunningham TS, Svetlov VV, Rai R, Smart W, Cooper TG.

I provided a simple template in my email to enter the annotations (I am unable to upload the template here). But basically provide annotations in the format:

Gene name [tab] GO Aspect [tab] GOID [tab] GO term [tab] Evidence [tab] With/From [tab] Qualifier [tab]comments <br>

Please send your annotations to me by November 3rd and also remember to name your sheet so i know who gave what. I will collate them and upload it on the wiki by Nov 5th. Each curator can send in individual sheets or each MOD can send their consensus sheet to me.

Collated Annotations

Collated annotations for

  • PMID 7568152 - Role of the GATA factors Gln3p and Nil1p of Saccharomyces cerevisiae in the expression of nitrogen-regulated genes. Stanbrough M, Rowen DW, Magasanik B.

Note about the PDF- when you open it you can barely read the text. Please zoom to read.
File:Jam7568152 Sheet2.pdf

  • PMID 8655543 - G1n3p is capable of binding to UAS(NTR) elements and activating transcription in Saccharomyces cerevisiae. Cunningham TS, Svetlov VV, Rai R, Smart W, Cooper TG.

File:Jam8655543.pdf

Minutes

Present: SGD- Rama, Karen, Julie, Jodi, Ruth, Rachael, Becky, Yasmin, Kimberly, Stan (RGD), Suzi, Pascale?

Announcements

1) The annotation conf.call and the Ref.genome conf. call are on two consequtive days (second Monday and second Tuesday of the month). If any of you have issues with this schedule please email Rama and Rachael.
2) If you have specific annotation related issues that you want discussed at this Annotaiton conf. call, please post them on this wiki page- http://gocwiki.geneontology.org/index.php/Topics_for_annotation_call. Rachael and Rama will review them and prioritize.

Papers for discussion

PMID 8655543 (GLN3 paper)

    • Is it appropriate to pick RNA Pol II terms although the paper doesn't mention RNA PolII? Yes, because all the nuclear protein coding genes are transcribed by RNA Pol II. Unless the paper mentions mitochondrial gene/plastid gene, POL II can be safely used. Of course if you can't tell and you are not comfortable go one level up.
    • The annotations from this paper are all in MF for GLN3. The paper shows data for function, how can you not make a Process annotation? It is okay to make an annotation to the term positive regulation of transcription from RNA Pol II... But this paper doesn't show evidence for the nitrogen catabolite repression part. So you have to stop with the positive regulation term. Also, based on inter-ontology relationship, a BP inference will be made from the MF annotation from this paper.
    • Ruth- new term request: positive regulation of organic nitrogen metabolic process by activation of transcription. Nitrogen in the media, vs stored nitrogen. Does it matter where the nitrogen is, what form? Is it true for multicellular organisms? Karen- The authors clearly state these genes are acting in NCR process. That is what we should go with.

If you were to make an annotation to this term the evidence code would be TAS and not IC because what is your inference based on (which GO Term?)

    • Annotation to promoter binding- txn binding site is upstream of promoter site. Authors don't show promoter binding.

The word promoter is loosely used. Karen and David are going to define core promoter and regulatory region binding terms.

Acceptable annotations from this paper:


You can make annotations to just GLN3 from this paper.
1077	sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in positive regulation of transcription from RNA polymerase II promoter	IDA
1077	sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in positive regulation of transcription from RNA polymerase II promoter	IMP
3700	RNA polymerase II regulatory transcription factor site sequence-specific DNA binding	IMP
3700	RNA polymerase II regulatory transcription factor site sequence-specific DNA binding	IDA

Okay if you annotated to:
 GO:0000978 - RNA polymerase II regulatory transcription factor site sequence-specific DNA binding |  IDA

PMID 7568152 (GAT/NIL1 paper)

Acceptable annotations from this paper:

FYI- NIl1 is an alias name for GAT1
GAT1 (NIL1)	F	1077	sequence-specific regulatory transcription factor site binding RNA polymerase II transcription factor activity involved in positive regulation of transcription from RNA polymerase II promoter	ISS with GLN3
GAT1 (NIL1)	P	1080	positive regulation of transcription from RNA polymerase II promoter by nitrogen catabolites	IMP	
GAT1 (NIL1)	P	1080	positive regulation of transcription from RNA polymerase II promoter by nitrogen catabolites	IGI	7568152	GLN3
GLN3	P	1080	positive regulation of transcription from RNA polymerase II promoter by nitrogen catabolites	IMP	7568152	
GLN3	P	1080	positive regulation of transcription from RNA polymerase II promoter by nitrogen catabolites	IGI	7568152	GAT1 (NIL1)

    • Appropriate level of granularity of P terms, i.e. why stop at nitrogen catabolites, and not go on to make terms for proline, glutamine, glutamate, etc.? Because it is not any different going down. The main idea of the paper is to show transcription in response to NCR.
    • Kimberly- Is there a way to add a comment for each term as to which system it is applicable/relevant to etc? Karen will check with David.