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

[mudshark]

if your modifications do not localize to a specific part of the genes
get average ChIPSeq counts for each gene and correlate with expression values

if your modifications do localize to a specific part of genes such as the transcription start site get average ChIPSeq counts for this specific region (e.g. -200 to +100 around the tss) of each gene and correlate with expression values.

important is a proper input chromatin normalization as expression has a strong correlation with the input chromatin reads (transcribed regions have more reads).