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

Question

[ankitplusplus]

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.

Answer 1

[Benn]

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

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

[pengchy]

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?

[Benn]

Why don't you try enrichment first?

findMotifs.pl

[pengchy]

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.

Answer 2

[zwdzwd]

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.