SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: Inferring transcription factor complexes from ChIP-seq data. Newsbot! Literature Watch 0 05-24-2011 02:00 AM
ChIP-Seq: DREME: Motif discovery in transcription factor ChIP-seq data. Newsbot! Literature Watch 0 05-06-2011 03:10 AM
ChIP-Seq: Diverse transcription factor binding features revealed by genome-wide ChIP- Newsbot! Literature Watch 0 12-24-2010 03:53 AM
PubMed: Extracting transcription factor targets from ChIP-Seq data. Newsbot! Literature Watch 0 06-26-2009 05:00 AM

Reply
 
Thread Tools
Old 11-23-2012, 04:34 AM   #1
Tjcooper
Junior Member
 
Location: Brighton

Join Date: Nov 2012
Posts: 1
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!

-TJ
Tjcooper is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:51 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO