Question: Co-occurring TF motifs in peak file from ChIP-seq experiment
gravatar for Dataminer
6.3 years ago by
Dataminer2.7k wrote:



I have peak file (3 column bed file) from a ChIP-seq experiment and I want to identify the transcription factor motifs that are present in these peaks and also which motifs are co-occurring.

Is their any approach/tool through which I can get this done. I know for identification of motifs it is quite straight forward to use any motif identification tool such as gimme motifs, meme etc, but the challenge is how to identify co-occurring motifs or compute them.


Thank you


motifs chip-seq • 2.9k views
ADD COMMENTlink modified 6.3 years ago by Ming Tang2.6k • written 6.3 years ago by Dataminer2.7k
gravatar for brentp
6.3 years ago by
Salt Lake City, UT
brentp23k wrote:

You could start with this paper: "Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices." They have a link to a sourceforge site to download some software.

There are also a lot of references in this paper about software that evaluates cooccurence: (disclosure: I am an author).

ADD COMMENTlink modified 13 months ago by RamRS30k • written 6.3 years ago by brentp23k
gravatar for Ming Tang
6.3 years ago by
Ming Tang2.6k
Houston/MD Anderson Cancer Center
Ming Tang2.6k wrote:

see this paper

ADD COMMENTlink written 6.3 years ago by Ming Tang2.6k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1331 users visited in the last hour