Question: list of enhacer for specific cell line
0
gravatar for na.cna30
5.1 years ago by
na.cna300
na.cna300 wrote:

Hello everyone:

I am looking for list of enhancers for different cell-lines in hg18. The enhancer files should include chr,start,end.

Could you help me to find them?thx

 

hg18 enhancer genome • 1.2k views
ADD COMMENTlink modified 4.7 years ago by chemcehn180 • written 5.1 years ago by na.cna300
1

I don't think there is a 'list' per se. But if you do a track search like this on UCSC Genome Browser, you get a total of 241 tracks (for hg18) that have the name enhancer associated with them. You can go through each of these tracks, filter and make a list yourself. 

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by komal.rathi3.5k

thanks for replying. can I ask how can download the selected track from table browser?it shows only in genome browser.

I am looking for stat1 in Hela cells with chromatin association marks.but can find it in UCSC. Is there any other database available for this purpose? 

ADD REPLYlink written 5.0 years ago by na.cna300
1

I did a track search using the keywords stat1 hela and it returned this. The 7th and 8th entries are available to download (you can see an inverted triangle following the name of the track, click on it to expand the track details and get the download link). One is a narrowPeak (BED format) file and the other is a bedGraph4 file. 

ADD REPLYlink written 5.0 years ago by komal.rathi3.5k
0
gravatar for chemcehn
4.7 years ago by
chemcehn180
Germany
chemcehn180 wrote:

Here is the list you are looking for:

http://enhancer.binf.ku.dk/presets/

It's in hg19, so you will have to use liftOver to convecr hg19 to hg18.

ADD COMMENTlink written 4.7 years ago by chemcehn180
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