Find TF target genes with integrate_ChIP_RNA()

[blahblahcodes12345]

I'd like to use the integrate_ChIP_RNA() function to find the targets of my TF of interest. I have the RNA-seq differential gene expression result (TF inhibitor drug vs. vehicle control RNA-seq data), but not sure what I should input for ChIP-seq data? I have ChIP-seq of the TF (both drug and vehicle control + IgG for each). I used MACS2 to call peaks. Not sure which files to input here for loadPeakFile(). Thank you for your help!

[blahblahcodes12345]

Thanks for a great package!

[blahblahcodes12345]

I also have the differential binding peak object (EdgeR/DESeq2) between drug vs. control ChIP-seq generated from DiffBindbut not sure if it's okay to use that as input

[shangguandong1996]

Sorry to reply so late :).

For me, I think call Peak using MACS2 during control is OK, but DE peak from drug vs control maybe better. Here is my reason.

First, we have to know why we need method like integrate_ChIP_RNA(). When finding the target of TF, RNA-seq diff result always have many noise, so many genes in the DE result maybe related with TF instead of the direct target. So we need the TF ChIP-seq to find the direct TF. For most experiment(maybe 99%), they just have a TF ChIP-seq(IP + Input). So for most user want to integrate TF ChIP-seq + RNA Diff, they will have RNA-seq(knock-down or out VS control) and a TF ChIP-seq (IP + Input).

But for you, if you have a TF inhibitor drug vs control ChIP-seq, it maybe have more accurate result. But please be sure to use the down region because you use the TF inhibitor drug instead of the TF induce drug.

Please feel free if you have more question :)

Best wishes Guandong Shang