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Filter human transcription factors

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!

transcription-factor rna-seq
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updated by jared.andrews07 jared.andrews07 • written by Chris • Chris

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

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written by Ram Ram

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()

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written by Chris • Chris

1 answer

This database has been the best I've found.

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written by jared.andrews07 jared.andrews07

Thank you so much!

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written by Chris • Chris

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

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written by Yogi • Yogi

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.

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written by jared.andrews07 jared.andrews07

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