Searching known TF binding sites for matching motif?

Xinlitik · 04-25-2013, 10:59 PM

Hi,

I have a list of DMRs that I have sent through MEME to identify common motifs. I would like to search known transcription factor binding sites for these motifs to see whether any of them correspond. Is there a tool that can do this? This is for humans.

Thanks!

Chrevan · 04-27-2013, 10:43 PM

You can try Homer, a tool for ChIP-Seq analysis, including Motif analysis, known motifs will be found.

crazyhottommy · 04-28-2013, 05:46 PM

what do you mean by "know transcription factor binding sites"?
if you mean the binding sites determined by ChIP-seq experimentally, I think you have to download the corresponding ChIP-seq data for corresponding TFs, peak call to generate a bed file, and just do a overlap with your DMRs to see any of them overlap.

you can do it through Galaxy or you can use bedtools.

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04-25-2013, 10:59 PM	#1
Xinlitik Junior Member Location: California Join Date: Nov 2012 Posts: 7	Searching known TF binding sites for matching motif? Hi, I have a list of DMRs that I have sent through MEME to identify common motifs. I would like to search known transcription factor binding sites for these motifs to see whether any of them correspond. Is there a tool that can do this? This is for humans. Thanks!

04-27-2013, 10:43 PM	#2
Chrevan Junior Member Location: Wuhan Hubei China Join Date: Jun 2011 Posts: 3	You can try Homer, a tool for ChIP-Seq analysis, including Motif analysis, known motifs will be found. __________________ Engineer of Data Analysis E-mail: chrevan2010@gmail.com

04-28-2013, 05:46 PM	#3
crazyhottommy Senior Member Location: Gainesville Join Date: Apr 2012 Posts: 140	what do you mean by "know transcription factor binding sites"? if you mean the binding sites determined by ChIP-seq experimentally, I think you have to download the corresponding ChIP-seq data for corresponding TFs, peak call to generate a bed file, and just do a overlap with your DMRs to see any of them overlap. you can do it through Galaxy or you can use bedtools.