ChIP-seq enrichment over specific genes

Question

[science_lizard]

I'm wondering if anyone knows a good program, perhaps on Bioconductor, that will help determine ChIP-seq enrichment over particular genes (would be wonderful if they would also be able to bin that enrichment over gene compartments like promotors, introns, etc.). For example, if I knock down a histone regulator, I'd like to show over specific genes that the mark is reduced in treatment vs control samples. Of course, I'd be happy to do this manually (i.e., making a box plot in R after calling ChIP-seq peaks, though I'm not sure what value would be best to plot), but Bioconductor packages do tend to be a bit more user-friendly for programming newbies like myself. Thanks in advance!

[ATpoint]

Why don't you perform a standard differential analysis, e.g. with DiffBind or csaw, and then check if the histone mark is significantly depleted at these genes (or its promoters). To illustrate this, I would probably plot the log2 read counts or the enrichments over input over these regions as a boxplot, one box per condition.

Answer 1

[Charles Warden]

If you have gene mappings, there may still be use for relatively standard gene enrichment tools (Enrichr, GATHER, DAVID, etc.)

Strictly speaking, I believe these programs are designed for ChIP-Seq enrichment:

GREAT

ChIP-Enrich: web-interface or Bioconductor package

However, if downstream targets are included among "sets of genes," I think the motif enrichment programs could also be useful:

i-cisTarget

HOMER

MEME Suite - includes GOMo for GO Motif analysis

Cistrome (SeqPos)