Hi,,
I'm completely new to the epigenetic field. My project is aiming to address the role of PRC2 on the two histone mark H3K27me3 and H3K4me3 in the treatment resistance mechanisms. Also, I would like to know the binding sites of the genes that are differentially expressed/ changed from treated and treated or the recurrent of the disease. I used ChromHMM to build the model and I get the segments for the samples. In addition I called the peaks and I have the mRNA expression of these data. I would like to know how can I use these files further for downstream analysis and mainly to understand how PRC2 or genes that are catalyses by PRC2 affecting the function of the histone mark and I would like to get the binding sites for these genes that interfere with this process.
Currently, I used the segment for ChromHMM along with peaks file and the expression data to see the expression patterns of the most significant peaks and how this changes from treated and un-treated samples. I will be happy to get more information/suggestions on how can I use the resulted files (chromHMM output/peaks file, expression) for further analysis.
Thanks,,
