There's a table that maps the UCSC ID's to Entrez Gene. Called something
like knownToLocusLink.

Michael

On Fri, Feb 4, 2011 at 11:37 AM, Arnaud Amzallag
<arnaud.amzallag@gmail.com>wrote:

> Dear IRanges / GenomicRanges / GenomicFeatures developers,
>
> first, thank you for these great packages, I use them a lot, because the
> are general and flexible enough, and yet very focused on genomic spaces.
>
> my question is in the title. I am glad to have a set of transcripts grouped
> by Entrez Gene IDs with the function transcriptBy(). However I would like to
> know what was the method and the rationale to create this association. The
> UCSC knownGene track, despite the name, is organized around transcripts
> rather than "genes". I cannot find this table on the UCSC genome website,
> neither I see documentation about it. I wold be glad to learn more about it.
>
> Best regards,
>
> Arnaud Amzallag
> Research Fellow
> Cancer center of the Massachusetts General Hospital
> Harvard Medical School
>
>

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