GSEA/fold change for ChIP-seq

Question

[yepeh72919]

Hello all, I have been reading some papers, and some of them make use of GSEA and the associated log fold change to quantify differentially expressed genes. I notice that most of these studies were conducted using RNA-seq, and not in ChIP-seq. My question is the following: do ChIP-seq analysis still make use of such tools for quantification?

I understand that the end goal of ChIP-seq is to find peaks and annotate them, but is there something that I am missing regarding understanding the downstream analysis in ChIP-seq vs RNA-seq?

Thanks a lot for your help!

[Prakash]

Apart from peak calling and annotation, ChIPseq data can also be used to find differential genomic regions across conditions. DiffBind performs such kind of analysis that internally uses DESeq2 for differential analysis. Similar to raw count for genes, Diffbind extracts raw counts for genomics regions (peaks) and further performs the differential analysis. Important here is you need to have replicates for ChIPseq data. Once you have differential sites fro given factor across the condition, you can annotate those regions and further compare with differentially expressed genes from RNASeq.