[BioC] GenomicFeatures : How Entrez gene IDs where associated to transcripts

[Arnaud Amzallag]

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