How to extract targets for specific TF from RegEnrich results

Question

[Fleur]

Hi all,

I am analysing my RNAseq data with RegEnrich, following the very well described pipeline as described here: Vignette RegEnrich

The analysis ends with the function

plotRegTarExpr(object, reg = "ARNTL2")

To plot any specific TF target in orange and its targets in black. Leading to a plot such as this:

I am wondering if there is a way/command to extract the names of the target genes for each TF? Thanks a lot, I hope someone can help

Answer 1

[Tao]

Hi,

If you have finished the "Regulator-target network inference" step, then you can simply access the full TF-target network by:

x = results_topNet(object)@elementset # The object is theRegenrichSet object

print(x)

Further, if you want to get the targets of some of the regulators (e.g. AATF and ABT1), then you can do it based on the basic R language:

subset(x@elementset, set %in% c("AATF", "ABT1"))

If you are interested in only one regulator (e.g., AATF), then

subset(x@elementset, set == "AATF")

The second column is the target genes.