Question: Download human ChIP-seq peaks other than ENCODE
0
gravatar for Kurui
3.3 years ago by
Kurui0
South Africa
Kurui0 wrote:

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

chip-seq • 1.4k views
ADD COMMENTlink modified 2.0 years ago by ZhouK.R.10 • written 3.3 years ago by Kurui0
0
gravatar for igor
3.3 years ago by
igor8.3k
United States
igor8.3k wrote:

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

ADD COMMENTlink written 3.3 years ago by igor8.3k

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

ADD REPLYlink written 3.3 years ago by Kurui0
0
gravatar for Ar
3.3 years ago by
Ar890
United States
Ar890 wrote:

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.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Ar890
0
gravatar for Kurui
3.3 years ago by
Kurui0
South Africa
Kurui0 wrote:

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.

ADD COMMENTlink written 3.3 years ago by Kurui0
1

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!

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Ar890

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!

ADD REPLYlink written 3.3 years ago by Kurui0
0
gravatar for ZhouK.R.
2.0 years ago by
ZhouK.R.10
Sun Yat-sen University, China
ZhouK.R.10 wrote:

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.

ADD COMMENTlink written 2.0 years ago by ZhouK.R.10
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