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