I am looking for a database from which I can download transcription factor binding sites ChIP-seq peaks. I already have those from ENCODE.
I am looking for a database from which I can download transcription factor binding sites ChIP-seq peaks. I already have those from ENCODE.
Roadmap Epigenomics - http://www.roadmapepigenomics.org/
Roadmap is mostly for histone modification data across ~120 human tissues. You can get a lot of TFBS data from GEO. However, I would like to know:
However, you may use DNase Hypersensitivity and TFBS prediction data to get a better list of TFBS sites based on tissues.
Thanks. I am looking to test how PWM generated from different sources (PBM, HT-SELEX, ChIP-chip, Promoters, Footprinting, e.t.c.) can be able to discriminate sequences with known binding sites from the background. So I want to expand the collection of ChIP-seq data that I have. These are the data from ENCODE that I am currently using.
I would recommend you to concentrate on a couple of TFs whose PWMs are established like CTCF, Fox proteins, Stat and see how their binding sites changes or is consistent with respect to different technology/sources. Do you think a big resource will help rather being focussed on a sets of particular TFs ?
Update: I think the following DREAM challenge could be of some help to you!
You should try ChIPBase (details are in this post), a comprehensive database for interpreting ChIP-seq data from multiple source, including ENCODE, GEO database. They also provided identified DNA-binding motifs and their regions of TFs.
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On it, thanks. Do you know if they have TFBS peak data?