Chip-Seq and Gene expression data

[paolo.kunder]

Dear All,

I am processing Chip-Seq data for 4 histone modifications in 3 samples.
I would like to find a way to correlate histone modifications to gene expression data,
any hint on how to do it?

thanks,
p

[markrobinsonca]

Depending on what you mean by "correlate" (and if you are an R user), we have a R/Bioconductor package called Repitools that can do some of this.

See (for general info):

http://www.bioconductor.org/packages/release/bioc/html/Repitools.html

The user's guide contains some examples:

http://www.bioconductor.org/packages/release/bioc/vignettes/Repitools/inst/doc/Repitools_vignette.pdf

For example, binPlots() or clusterPlots (or their output) can be useful for various exploratory tasks.

Best regards,
Mark

[paolo.kunder]

Hi,
I mean that I have some list of genes found to be differentially expressed between two conditions with microarray analysis.

I have also some list of genes whose histone modifications ( activating and repressing transcription) vary betweend the two conditions.

I would like to find a way to check wheter they correlate, for example,

gene condition A condition B
x 10 8
y 98 200

histone mod gene condition A condition B

H3K4me(act) x 20 reads 12 reads
H3K27me3(rep) x 34 reads 50 reads

In this case gene x is found to be turned off with microarray data and also ChipSeq data confirm that these genes is subjected to histone repression ( decrase of H3K4me3 and increase of H3K27me3)


any hint?

thanks,
p