RefGenome8Jul08 Phone Conference (Archived): Difference between revisions
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==General points== | ==General points== | ||
* From [http://sourceforge.net/tracker/index.php?func=detail&aid=1903284&group_id=36855&atid=1040173 TNNT2] discussion; Susan : This raises the question of how best to handle paralogs. The 3 human genes TNNT1,2,3 cluster in InParanoid with a single fly | * From [http://sourceforge.net/tracker/index.php?func=detail&aid=1903284&group_id=36855&atid=1040173 TNNT2] discussion; Susan : This raises the question of how best to handle paralogs. The 3 human genes TNNT1,2,3 cluster in InParanoid with a single fly troponin protein (encoded by up). up has the best InParanoid score with TNNT3 so this was what I declared as ortholog in the spreadsheet (pending the review of ortholog determination). However, this is probably misleading | ||
troponin protein (encoded by up). up has the best InParanoid score with | - from a tree (e.g. treefam) it is clear that the duplication in human occurred after the fly/human divergence. Is it better to enter in the fly gene multiple times in the spreadsheet for gene human paralog? | ||
TNNT3 so this was what I declared as ortholog in the spreadsheet (pending | (Pascale: Note that Kara's ortho MCL analysis puts up with TNNT2) | ||
the review of ortholog determination). However, this is probably misleading | |||
- from a tree (e.g. treefam) it is clear that the duplication in human | |||
occurred after the fly/human divergence. Is it better to enter in the fly | |||
gene multiple times in the spreadsheet for gene human paralog? | |||
==Next conference call== | ==Next conference call== | ||
Revision as of 09:28, 24 June 2008
Tuesday July 8, 2008, 1 PM CDT, 11 AM PDT, 7 PM BST
Review old/ongoing action items
DONE:
- Seth: send URL sometime to the prototype of the ortholog tool this week (will do!)
- [Action item]: MGI: verify GRIN1 annotation binding/complex
Ongoing:
- All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1]
see also Annotation_QC for some general documentation and previous issues
- All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.
- All (ongoing): Develop annotation SOPs
There are some wiki pages about that on the ref genome main page's annotation section: Reference_Genome_Annotation_Project#Gene_Annotation
[Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs. [Action item]: Discuss use of binding/regulation terms (GOC meeting)
Source Forge QC discussion
General points
- From TNNT2 discussion; Susan : This raises the question of how best to handle paralogs. The 3 human genes TNNT1,2,3 cluster in InParanoid with a single fly troponin protein (encoded by up). up has the best InParanoid score with TNNT3 so this was what I declared as ortholog in the spreadsheet (pending the review of ortholog determination). However, this is probably misleading
- from a tree (e.g. treefam) it is clear that the duplication in human occurred after the fly/human divergence. Is it better to enter in the fly gene multiple times in the spreadsheet for gene human paralog? (Pascale: Note that Kara's ortho MCL analysis puts up with TNNT2)
Next conference call
Tuesday August 12, 2008, 10 AM CDT (8 AM PDT, 4 PM BST)
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