Question: (Closed) Assess Significant Overlap In Chip Datasets
0
gravatar for enricoferrero
6.7 years ago by
enricoferrero770
United Kingdom
enricoferrero770 wrote:

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,

ADD COMMENTlink written 6.7 years ago by enricoferrero770
1

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

ADD REPLYlink written 6.7 years ago by Pierre Lindenbaum120k

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.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by enricoferrero770

and what would be your source of encode DATA ?

ADD REPLYlink written 6.7 years ago by Pierre Lindenbaum120k

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?

ADD REPLYlink written 6.7 years ago by enricoferrero770
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1881 users visited in the last hour