RefGenome8Jul08 Phone Conference (Archived)

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


  • Pascale dictyBase
  • Kimberly wormbase
  • Ranjana wormbase
  • Kara ppod
  • Mike SGD
  • Ruth
  • Tanya TAIR
  • Donghui TAIR
  • Emily GOA
  • Petra dictybase
  • Jim Hu
  • Seth
  • Victoria RGD
  • Susan flybase
  • Judy MGI

Electronic jamboree

Review old/ongoing action items


  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


  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)

PPOD update

Our programmer is back from leave and will be rolling out several new features to the PPOD web interface as soon as tomorrow.

I need to check in with Paul to see where they are, and whether we should start a new OrthoMCL and Jaccard run from the gp2protein/fasta files that he has used for PANTHER analysis.


Source Forge QC discussion

General points

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)


Ranjana [[2]]


Stacia [[3]]

Next conference call

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

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