Hi all,

    I have a DE gene dataset and I would like to know which TFs have binding sites at the promoters of these genes. I found a list of 615 human TFs on the GSEA website with the genes they bind to, but my DE gene list is too large to manually test. I then thought to create custom GO terms using each the TF target genes, but that also would take too long (615 TFs). Does anyone have any good alternative suggestions? All I want to do is to mine the TFs that could potentially bind to my DE genes to validate them functionally. Thanks in advance!

If you are only interested in the DE genes from your data set, you could consider the over-representation test on your TF geneset. You can use the hypergeometric test implemented in enricher() function of the clusterProfiler package and MSigDB's C3 TFT geneset. HTH.