Filter human transcription factors

Question

[Chris]

Hi Biostars,

I have a list of genes that differential expressed in RNA-seq and would like to filter only transcription factors. Do we have any tools or good way to do this? Thank you so much!

[Ram]

What have you tried? Have you looked at GO annotations?

[Chris]

Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 The things I am quite confuse is there are many different pathway when I use GO, GSEA or using different database such as KEGG or others, so not sure which pathway I should focus on. I found there are many functions that perform pathway analysis such as fgsea(), gseGO(), gseKEGG(), enrichGO()

Answer 1

[jared.andrews07]

This database has been the best I've found.

[Alex Reynolds]

Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resources/motif_clustering

[jared.andrews07]

That's a nice resource. Motif redundancy is by far the most frustrating aspect of motif analyses, in my experience. To a degree, we address it by filtering via expression, but it still results in imperfect results.

[Chris]

Thank you so much!

[Yogi]

Definitely the best resource. Was also going to recommend this one.