Hi Rileen, your observation is correct, the Ensembl genes table ensGene does not include ensembl gene IDs but transcript IDs. (this a documentation error: the field "name" of "ensGene" is documented as "name of gene" but should be "name of transcript") This actually makes sense, because the table indicates the positions on the genome, and a gene in Ensembl's nomenclature is just a collection of transcripts and not located by itself on a genome. Transcripts are located on a genome, each transcript sequence ID is assigned to protein sequence ID and many transcripts are assigned to a gene model. Therefore, a second table is used in the UCSC genome browser, just like in Ensembl, to link transcripts to gene identifiers. By using the table browser, I see that the table "ensGtp" links the transcript ID to protein and gene IDs, so if you need the gene model ID for the transcript IDs, you can use the table browser, output format = "selected fields from primary and related tables" and in the following dialog, select all fields from the ensembl genes table and the column geneId from the ensGtp table. You should obtain the ensembl transcripts coordinates with their respective gene ids as a table in this way.
good luck, cheers Max On Fri, Jan 21, 2011 at 9:54 PM, Rileen <[email protected]> wrote: > Dear UCSC Genome Browser team, > As always, thanks > for the wonderul > tool that the UCSC genome browser is. > > I downloaded the ensGene tables for hg18 and hg19 - the gene_id > seems to synonymous with transcript_id, and there are no ids starting > with ENSG, which is what I would expect for Gene IDs, as opposed to > Transcript IDs, for which ENST makes sense. > > Is this some recent change, or am I missing something? > > Looking forward to your reply, > Yours, > Rileen > > -- > ****************************************************************** > "I know nothing, but i _know_ that." > > Rileen Sinha [email protected], [email protected] > ****************************************************************** > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
