Question: GSEA using TFs as the gene set
0
gravatar for tkapell
9 months ago by
tkapell0
University of Bonn, Germany
tkapell0 wrote:

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!

  

ADD COMMENTlink modified 9 months ago by lhuang730 • written 9 months ago by tkapell0
Answer: GSEA using TFs as the gene set
0
gravatar for lhuang7
9 months ago by
lhuang730
United States
lhuang730 wrote:

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.

ADD COMMENTlink written 9 months ago by lhuang730

Thank you lhuang7. May I ask what is the difference between the two?

ADD REPLYlink written 9 months ago by tkapell0
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