FANTOM5 TSS downloads by cell line
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7.2 years ago
drautuna ▴ 60

Hi, I have a simple question to those of you familiar with using the fantom5 database on enhancers, promoters, and TSS's. I am currently in a project where I annotate variants, one of which is based on whether they fall into regions of importance, such as enhancers and TSS.

I'm supposed to use the fantom5 database for enhancers and TSS's for certain cell lines; I've found that the fantom5 enhancers were simple enough to find on their website by cell line, simply going through the data page:

http://fantom.gsc.riken.jp/data/

and then to the transcribed enhancer atlas

http://enhancer.binf.ku.dk/Pre-defined_tracks.html

which was extremely handy in finding enhancers by the several cell lines I need. 

However, I'm having trouble finding a download page for the TSS's by different cell/tissue lines, seeming to be quite more difficult to find. Can someone give me a download link? thanks.

fantom5 cell lines data • 5.6k views
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Entering edit mode

Hi, 

Note that TSSs (TSS regions or CAGE peaks) and enhancers are defined based on a (sub)set of CAGE profiles (samples or cell lines) in general. Their activities in a profile can be measured by intersecting raw signals, such as CTSS BED files (corresponding to read counts starting from each 1bp) available at:

http://fantom.gsc.riken.jp/5/datafiles/latest/basic/

Activities of TSSs (CAGE peaks) have been calculated below:

http://fantom.gsc.riken.jp/5/datafiles/latest/extra/CAGE_peaks/ 

which is also hyperlinked from http://fantom.gsc.riken.jp/data/ .

 

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