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How can i find the regualatory transcription factor of my list of gene

Hi,

I have some list of human genes and i wanted to find all transcription factor associated with these genes. What software tools, database i can used for finding such regulatory TF.

transcription factor regulatory genomics gene
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updated by zwdzwd zwdzwd • written by ankitplusplus • ankitplusplus

2 answers

You can try Homer, it searches for enriched TF sites in your gene set.

http://homer.salk.edu/homer/

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written by Benn Benn

Hi b.nota, the scanMotifGenomeWide.pl script give many binding sites. Is it possible to rank the result according to the sixth column, which is the log odds ratio?

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written by pengchy pengchy

Why don't you try enrichment first?

findMotifs.pl
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written by Benn Benn

Hi b.nota, I have run findMotifs.pl and got the enriched motifs. Then I want to know which target gene these enriched motifs can regulat, so the scanMotifGenomeWide.pl was run.

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written by pengchy pengchy

Ensembl regulation database has a collection of TFBS sites for human and mouse. ftp://ftp.ensembl.org/pub/release-85/regulation/homo_sapiens/

You can overlap that with your gene coordinates.

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written by zwdzwd zwdzwd

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