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Old 04-25-2013, 10:59 PM   #1
Xinlitik
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Default 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!
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Old 04-27-2013, 10:43 PM   #2
Chrevan
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You can try Homer, a tool for ChIP-Seq analysis, including Motif analysis, known motifs will be found.
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Old 04-28-2013, 05:46 PM   #3
crazyhottommy
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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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