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Old 06-24-2012, 10:32 PM   #1
Location: Australia

Join Date: Sep 2009
Posts: 14
Default Comparing ChIP-seq from different transcription factors / different cell lines


I was wondering, when I compare the ChIP-seq peaks from either different transcription factors or same factors but different cell lines (but same species), how much overlap is to expect or what overlap would be considered as significant or irrelevant etc... ??
I struggle to interpret the percentage of overlap and I'm generally not sure how important such comparisons are, if you can really draw any conclusions.
Just an example: I get 30% overlap of two different ChIP-seq datasets with the same factor but in different cancer cell lines and 30% overlap of peaks obtained in the same cell line but looking at 2 different transcription factors (although the factors belong to the same family and are known to heterodimerise).
I'm writing up my PhD thesis at the moment and need to elaborate on the ChIP-seq analysis, that's why I even started looking at other datasets and performing comparisons.

It would be great if someone can help me or share their opinion on this topic.

Thanks, Jeannine
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Old 06-24-2012, 11:43 PM   #2
Location: Germany

Join Date: Dec 2010
Posts: 29

Please read this

You may also need to look at DiffBind from Bioconductor as well as
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