Promoter Or Enhancer Regions Bed Format

Question

[win]

Hi all, One can download a BED file of human genome with exonic and intronic chromosomal coordinates.

I wanted to know if there is such a file for promoter or enhancer sites, best if it was in BED format.

Thanks in advance. A

Answer 1

[Ryan Dale]

UCSC has tracks for ChromHMM (segmentation by HMM, from ENCODE/Broad) which use multiple histone modifications in a hidden markov model to call enhancer regions as well as other regions (including active, weak, and inactive promoters) for a total of 15 classes in 9 cell lines.

Using the Table Browser, the data are in the "Regulation" group and "Broad ChromHMM" track. The BED format output indicates the class in the "name" field.

[dfernan]

Also if you have your own experiment, and several histones modifications you can use ChromHMM to segment the genome in the regions mentioned above - the software is available at http://compbio.mit.edu/ChromHMM/

Answer 2

[dfernan]

Hi, active enhancer regions are generally called as regions where h3k27ac and h3k4me1 modifications are present so it depends on the cell type and therefore on the specific experiment you are analyzing.

With respect to promoter regions it's easier, you can download a gene annotation file and then write your own script to call promoters (generally defined as +/- 2kb from TSS).... or use galaxy (download within galaxy a gene annotation from ucsc and then use galaxy to process the file and extract the promoters)

[samsara]

how can i extract promoters in galaxy once i load bed from from UCSC ?

Answer 3

[Ian]

For enhancers take a look a VISTA Enhancer browser.

For promoters the following link might help, which describes ways of obtaining them from UCSC Genome Browser:

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download18