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Assess Significant Overlap In Chip Datasets

Hi,

I'm looking for methods and/or tools that can be used to assess overlap between ChIP (ChIP-ChIP or ChIP-Seq) datasets.

Being a drosophilist I have access to several ChIP datasets at modENCODE and BDTNP and I'd like to know if some of these transcription factor binding profiles show a significant overlap with the one I produced for my transcription factor of interest. The idea is to make hypotheses about possible cofactors.

Bonus points if the tools also help in the visualisation of the overlap and significance and if they're R or Bioconductor-related.

What are your suggestions Biostar?

Thanks a lot,

chip-seq overlap visualization bioconductor
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written by enricoferrero enricoferrero

I've never used the Chip-* technology , what does a "dataset" look like ?

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written by Pierre Lindenbaum Pierre Lindenbaum

There are different file formats out there (sgr, wig, bed, gff...) but they're all basically binding interval coordinates, like:

chr2R 10678 10942
chr3R 3258 4566
...

which means that your TF is binding in those regions of the genome.

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written by enricoferrero enricoferrero

and what would be your source of encode DATA ?

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written by Pierre Lindenbaum Pierre Lindenbaum

I'm not sure I understand the question. I can download data from the modENCODE website and extract binding intervals coordinates for every dataset I'm interested in. Does that answer your question?

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written by enricoferrero enricoferrero

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