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Old 03-25-2014, 07:31 AM   #1
Location: Freiburg

Join Date: Oct 2012
Posts: 56
Default Correlating/clustering RNA-seq with ChIP-seq data?

Hi everyone,

I have RNA-seq data from adipocytes, where a certain gene, that is involved in heterochromatin, is knocked out. I would like to correlate/cluster this dataset with another dataset, where we have ChIP-seq for H3K9me3.

Basically, I would like to see if those genes that are upregulated in my knockout samples are the one that are enriched for H3K9me3.

I have tried to search the forum here and have read several posts about the topic, but I am still not sure how to go about it and what packages to use.

Thanks a lot! Appreciate your help.

// Kevin
DonDolowy is offline   Reply With Quote
Old 03-25-2014, 09:09 AM   #2
Location: Münster, Germany

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I know the TargetCaller package for R, but this is mainly for transcription factors. Whether it is suited for Histon ChIP-data you have to test.
Thias is offline   Reply With Quote
Old 03-25-2014, 10:00 PM   #3
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Location: Sydney, Australia

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Have a look at the "Integrative analysis of epigenetics and gene expression" section of the Repitools manual. The heatmap plot is what you want to use.
Dario1984 is offline   Reply With Quote
Old 03-26-2014, 02:48 AM   #4
Location: Cambridge, UK

Join Date: Aug 2008
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There's also the Rcade package in Bioconductor (R-based analysis of ChIP-seq And Differential Expression)...
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