Co-occurring TF motifs in peak file from ChIP-seq experiment

Question

[Dataminer]

Hi!

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

Answer 1

[brentp]

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: http://bib.oxfordjournals.org/content/early/2013/08/15/bib.bbt053.abstract (disclosure: I am an author).

Answer 2

[Ming Tommy Tang]

See this paper.