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). 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
