Tool Or Technique To Find Co-Occuring Motifs Within Genomic Intervals That Correspond To Tf Binding Regions.
4
2
Entering edit mode
11.2 years ago
ChIP ▴ 600

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

chip-seq • 6.3k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
11.2 years ago
Chris Whelan ▴ 570

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

ADD COMMENT
2
Entering edit mode
11.2 years ago
Ying W ★ 4.3k

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'.

ADD COMMENT
1
Entering edit mode
11.2 years ago
Ian 6.1k

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.

ADD COMMENT
0
Entering edit mode
11.2 years ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 2072 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6