RefGenome8Jul08 Phone Conference (Archived)
Tuesday July 8, 2008, 1 PM CDT, 11 AM PDT, 7 PM BST
- Pascale dictyBase
- Kimberly wormbase
- Ranjana wormbase
- Kara ppod
- Mike SGD
- Tanya TAIR
- Donghui TAIR
- Emily GOA
- Petra dictybase
- Jim Hu
- Victoria RGD
- Susan flybase
- Judy MGI
- Stacia SGD
- select genes or papers? and annotate together
- US people should annotate on Thursday and UK people on Friday; we'd all meet Friday (8 AM in California; 4 PM in UK)
- topics: elongation factors or housekeeping genes
- Emily will put together a suggestion list for genes to annotate
- we'll do this by webex and phone conference
Review old/ongoing action items
- Seth: send URL sometime to the prototype of the ortholog tool this week (will do!)
- [Action item]: MGI: verify GRIN1 annotation binding/complex
- All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table 
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)
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.
Integrating ref genomes in AmiGO
(Seth) As discussed on the call last month, I wanted to give links to the current implementation of the Ref Genome information that we're going to be putting into AmiGO. The page explaining the current state is at:
I also have setup a wiki page to help keep track of the development of and feedback for the Ref Genome in AmiGO. You might want to take a look at it before commenting:
This is still a work in progress, so there may be downtime and sudden changes. Thank you in advance for any feedback.
Source Forge QC discussion
- From TNNT2
- see also RefGenome11Mar08_Phone_Conference#2._TNNT2 March 2008 discussion; not sure of the resolution.
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)
- Maybe the tree view will solve this
- Annotations to xx binding can be ISS'ed
- wormbase happy to keep IEAs for things like 'protein kinase activity'; unsure that function is conserved
- transferring CC annotation?
- transferring Processes by ISS can be tricky
Next conference call
Tuesday August 12, 2008, 10 AM CDT (8 AM PDT, 4 PM BST)
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