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Old 11-23-2012, 04:34 AM   #1
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Location: Brighton

Join Date: Nov 2012
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Default Correlation of CHiP-Seq with ENCODE transcription factor data

Good afternoon

I am currently an undergraduate student of molecular biology carrying out my final year dissertation project. The group I am working with have carried out a global ChIP-seq and microarray study centred on a specific non-DNA binding viral protein and I have been using chromosome conformation capture techniques to probe mechanisms by which this protein regulates target genes.

As this protein does not bind DNA directly, as a small side project, I also want to identify potential candidates for targeting factors. A few are currently known but many are likely left to be found.

I was wondering if there was a automated way to use the ENCODE transcription factor data to pull out a list of factors which associate at the same loci as this viral factor. I could do this manually via the UCSC genome browser but of course this would be very time consuming and I could not do it on a global level. I also understand this is a rather bias and simplistic approach but i'm only looking for a basic starting point to look for factors which may warrant further investigation.

Many thanks for any help!

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