Question: Enhancers in Introns
0
gravatar for kyeemon7
13 months ago by
kyeemon70
kyeemon70 wrote:

Can someone help me to identify potential enhancers located within the introns of genes within the human genome: chr22:30,000,000-35,000,000 (2009 assembly, hg19) that are differentially active in HUVECs vs NHLFs. I'm not sure what track to use in the UCSC browser or how to find data in the introns only.

human intron enhancer gene • 587 views
ADD COMMENTlink modified 12 months ago by ajsn6c0 • written 13 months ago by kyeemon70
1
gravatar for Charles Plessy
13 months ago by
Charles Plessy2.2k
Japan
Charles Plessy2.2k wrote:

Perhaps you can find useful information in the FANTOM5 project's transcribed enhancers atlas? Here is a link to your region of interest in our ZENBU genome browser view. The track of interest is called _FANTOM5 Human permissive enhancers phase 1 and 2_.

ADD COMMENTlink written 13 months ago by Charles Plessy2.2k
1
gravatar for WouterDeCoster
13 months ago by
Belgium
WouterDeCoster22k wrote:

Another valuable resource is the Roadmap epigenomics browser: http://egg2.wustl.edu/roadmap/web_portal/

ADD COMMENTlink written 13 months ago by WouterDeCoster22k
0
gravatar for ajsn6c
12 months ago by
ajsn6c0
ajsn6c0 wrote:

We use H3K4me1 and H3K27ac overlaps as putative enhancer marks. You can use Bedtools IntersectBed to overlap the two. You can download the histone peaks from UCSC Genome Browser, then use HOMER annotation to annotate the peaks and filter for introns.

ADD COMMENTlink modified 12 months ago • written 12 months ago by ajsn6c0
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