Tool Or Technique To Find Co-Occuring Motifs Within Genomic Intervals That Correspond To Tf Binding Regions.

Question

[ChIP]

Hi!

I have a list of transcription factors (along with their PWM) for which I want to check if they are co-occurring in my peaks (TF bound DNA region obtained from ChIP-Seq expts).

Does anyone knows about a tool which can do that. Even a web-based tool is fine.

Thank You

[Istvan Albert]

what do you mean by ChIP-seq profile? What type of data do you have.

[ChIP]

I have edited the question. please have a look again.

Answer 1

[Chris Whelan]

It looks like ChIPModule is designed to do that:

http://hulab.ucf.edu/research/projects/ChIPModule/index.html

Also, I think that Homer can help with this, although I've only used it for finding enriched motifs, rather than co-enriched motifs. It was very straightforward to use for the simpler task, at least.

http://biowhat.ucsd.edu/homer/chipseq/peakMotifs.html

Answer 2

[Ying W]

Here are some more tools:

http://pubmed.gov/22422841 "Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection"

http://pubmed.gov/22156162 "RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets"

You might want to search around for 'cis regulatory modules' or 'co-occurring motifs'.

Answer 3

[Ian]

If you are interested in a statistical answer to your question ("Do the two motif sets co-occur?") you could enter the coordinates of the matching sites to each motif (two files of BED coordinates) in the Genomic Hyperbrowser.

I also spotted this a while back (but have not used it): COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets.

Answer 4

[cristianrohr768]

Yoy can create a fasta file from the chip BED file using the fastaFromBed module in the bedtools package

then use INSECT http://bioinformatics.ibioba-mpsp-conicet.gov.ar:84/INSECT/ http://www.ncbi.nlm.nih.gov/pubmed/24008418

with your desired TFs