RefGenome8Jul08 Phone Conference (Archived): Difference between revisions

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==Source Forge QC discussion==
==Source Forge QC discussion==
===General points==
==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
* 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
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- from a tree (e.g. treefam) it is clear that the duplication in human
- 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
occurred after the fly/human divergence. Is it better to enter in the fly
gene multiple times in the spreadsheet for gene human paralog?  
gene multiple times in the spreadsheet for gene human paralog?
 
 


==Next conference call==
==Next conference call==

Revision as of 09:26, 24 June 2008

Tuesday July 8, 2008, 1 PM CDT, 11 AM PDT, 7 PM BST

Review old/ongoing action items

DONE:

  1. Seth: send URL sometime to the prototype of the ortholog tool this week (will do!)
  2. [Action item]: MGI: verify GRIN1 annotation binding/complex

Ongoing:

  1. 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

  1. 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.
  1. 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?

Next conference call

Tuesday August 12, 2008, 10 AM CDT (8 AM PDT, 4 PM BST)

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