Thanks for the clarification and the tip!
Wishing you a great Sunday,
Yours,
Rileen
On 23 January 2011 14:23, Maximilian Haussler <[email protected]> wrote:
> 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
>>
>
>
--
******************************************************************
"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
