GSEA using TFs as the gene set
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thkapell ▴ 10
@tkapell-14647
Last seen 14 months ago
Helmholtz Center Munich, Germany

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!

  

GSEA transcription factor binding site enrichment analysis • 1.2k views
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lhuang7 ▴ 50
@lhuang7-7824
Last seen 3.9 years ago
United States

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.

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

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