Download human ChIP-seq peaks other than ENCODE

Question

[Kurui]

I am looking for a database from which I can download transcription factor binding sites ChIP-seq peaks. I already have those from ENCODE.

Answer 1

[igor]

Roadmap Epigenomics - http://www.roadmapepigenomics.org/

[Kurui]

On it, thanks. Do you know if they have TFBS peak data?

Answer 2

[ATRX]

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:

1. What is the aim of your project ?
2. What are looking for ? to help you better in terms of getting the datasets.

However, you may use DNase Hypersensitivity and TFBS prediction data to get a better list of TFBS sites based on tissues.

Answer 3

[Kurui]

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.

[ATRX]

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!

[Kurui]

I have focused on the most established TFs already. So I am now expanding the set to check if my conclusions still hold. Thank you very much for the link. That is definitely something I am interested in.

Thanks again!

Answer 4

[ZhouK.R.]

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.