Question: Co-occurring TF motifs in peak file from ChIP-seq experiment
1
gravatar for Dataminer
5.3 years ago by
Dataminer2.6k
Netherlands
Dataminer2.6k wrote:

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

 

motifs chip-seq • 2.6k views
ADD COMMENTlink modified 5.3 years ago by Ming Tang2.5k • written 5.3 years ago by Dataminer2.6k
2
gravatar for brentp
5.3 years ago by
brentp23k
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: http://bib.oxfordjournals.org/content/early/2013/08/15/bib.bbt053.abstract (disclosure: I am an author).

ADD COMMENTlink modified 4 weeks ago by RamRS24k • written 5.3 years ago by brentp23k
1
gravatar for Ming Tang
5.3 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

see this paper http://nar.oxfordjournals.org/content/early/2013/12/09/nar.gkt1288.full

ADD COMMENTlink written 5.3 years ago by Ming Tang2.5k
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