Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Mapping genomic regions promoter 3' UTR exon etc mathew Bioinformatics 0 05-10-2012 07:19 AM
Promoter regions hg19 NearyJL78 Bioinformatics 2 05-16-2011 12:08 PM
Length exon, intron, promoter and intergenic regions in human genome khb Bioinformatics 1 01-17-2011 02:03 PM

Thread Tools
Old 07-19-2012, 12:10 PM   #1
Location: Cupertino, CA

Join Date: Nov 2011
Posts: 59
Default Promoter or enhancer regions BED format

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
ashkot is offline   Reply With Quote
Old 07-20-2012, 09:05 AM   #2
Junior Member
Location: MD

Join Date: Jul 2011
Posts: 9

UCSC genome browser -> genome of choice (hg18 or hg19) -> Tables -> Groups(Genes...) -> Track (RefSeq)

When you output you have the option of selecting the format (bed) and can pick whether you want the whole gene (you can then parse out the exons) or some distance up or downstream of the genes (so, say 2000bp upstream of the 5' end would be a promoter area).

If you want enhancers you can use a track with the histone methylation/acetylation marks that correspond to enhancers (I always forget which one it is - h3k27acetylation?)
thedavid is offline   Reply With Quote
Old 01-26-2014, 05:20 PM   #3
Junior Member
Location: Taiwan

Join Date: Nov 2013
Posts: 4
Default enhancer associated gene


I have peaks which are overlapping with enhancer regions. Now, my question is which gene are regulated by these enhancers. Therefore, I need idea how can I retrieve information of genes of related enhancers. (any tool or something!!)

zyie is offline   Reply With Quote
Old 01-27-2014, 10:56 AM   #4
Location: USA

Join Date: Mar 2010
Posts: 50

Try using the more recent Encode-derived annotation at Ensembl.
m_two is offline   Reply With Quote
Old 01-28-2014, 04:38 AM   #5
Location: Stockholm

Join Date: Apr 2013
Posts: 42

Usually the closest genes surrounding the enhancer region are more likely to be regulated by such enhancer. This is the general assumption used in most papers I read about enhancers.
ge2sasag is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:50 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO