Hg19 Promoters .Bed File

Question

[Jneary1978]

Is there already a pre-defined downloadable list of all predicted promoters in the human genome? Preferably a .bed file? I'm not having a lot of luck finding anything.

If not, can you suggest resources to obtain this info?

Thanks!

Answer 1

[Casey Bergman]

If you define X kb upstream of a gene to be a promoter, you can get this using the UCSC table browser as follows:

• 1) Go to: http://genome.ucsc.edu/cgi-bin/hgTables
• 2) Click "Get Output"
• 3) Select the Upstream by X bp radio button
• 4) Enter your cutoff for length upstream of gene start
• 5) Click "get BED"

[Rob]

There's also the Ensembl annotation data - this contains more information on transcripts and exon boundaries too.

But to my knowledge, there's no definitive definition of promoter X being 2kb in length, and promoter Y being 1.5kb. We just have to make a judgment on what's an appropriate size.

[Jneary1978]

Thank you much!