At 16:01 +0000 9/2/07, Bert Overduin wrote:
Damian,
OTTHUMG00000131472 is not an "ordinary" Vega gene, but a CORF gene:
<http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000131472&db=core>http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000131472&db=core
<http://vega.sanger.ac.uk/info/data/corf.html>http://vega.sanger.ac.uk/info/data/corf.html
I guess we don't include these in Ensembl. I mailed Val to ask, but
didn't hear anything yet ....
Its a corf gene, but it doesn't have a GD prefix, so I think it
should have been included... Steve T should have the definitive
answer on what happened though. Might have just not got transfered
due to assembly diffs.
Tim
Cheers,
Bert
On 9 Feb 2007, at 15:55, Damian Smedley wrote:
On Fri, 9 Feb 2007, Amir Karger wrote:
If I do a query in Biomart for Vega Gene IDs:
OTTHUMG00000131472
OTTHUMG00000017411
I get the second (BRCA2) but not the first (YES1). Any idea why? YES1 is
on chr18, so it's not one of the chromosomes Vega is missing (2, 4, 5,
11). I think part of the problem may be on Ensembl's side: they don't
associate YES1 with the corresponding OTT number
(<http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000176105>http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000176105),
even though the Vega website does
(<http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000131472&;>http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000131472&;
db=core).
Seems OTTHUMG00000131472 is not in homo_sapiens_vega_42_36d and therefore
nowhere within the main ensembl site or biomart. Anyone know why this id
appears on the vega website but not ensembl's?
Thanks
Damian
I believe I could find other examples if necessary. In related or
unrelated news, Biomart 'count' finds only 57 genes with HUGO IDs on
chr18, even though I'm pretty sure there are many more. (I wrote 250 in
an email, though I don't remember how I got that number.)
Thoughts?
- Amir Karger
Research Computing
Life Sciences Division
Harvard University
617-496-0626
Bert Overduin, Ph.D.
Ensembl Helpdesk Officer
EMBL Outstation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Tel. + 44 1223 494462
Fax +44 1223 494468
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Hinxton Fax: +44 1223 496802
Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/Users/th
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