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

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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
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Old 03-25-2014, 09:09 AM   #2
Thias
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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.
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Old 03-25-2014, 10:00 PM   #3
Dario1984
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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.
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Old 03-26-2014, 02:48 AM   #4
rory
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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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