Integrating mRNA expression data with chips data to get the epigenetic profiles of H3k27me3, H3K4me3 and EZH2 in GBM

Question

[munaj86]

Hi,,

Can anyone recommend/suggest an approach that I can use to integrate the mRNA expression data with chipseq data to understand how the epigenetic profiles changes from primary and recurrent samples. So, I have TSS expression data and a chips data. I post-processed the chips data and I apply ChromHMM to get the chromatin state across the samples. I would like to know how can I used these data to find the pattern of histone modification changes across cells and how can I correlate this with mRNA expression data.

Thanks,,

Muna

Answer 1

[jared.andrews07]

You could try ChromDiff, but it hasn't been updated since 2016. It seems to try to do exactly what you're asking though, so probably worth a shot. There's also EpiAlign, though how to use it isn't very clear.

If you can't get those to work, my guess is you will have to write some code to do this yourself.