On Fri, 9 Feb 2007, 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), > > even though the Vega website does > > (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?
as a follow up we seem to have OTTHUMG00000068164 which is the same gene but annotated from a different source in ensembl and biomart. Does someone want to explain the policy for which vega genes get into the vega database ensembl uses. Thanks Damian > > 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 > > >
