Question: How can i find the regualatory transcription factor of my list of gene
1
gravatar for ankitplusplus
3.9 years ago by
ankitplusplus30 wrote:

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.

ADD COMMENTlink modified 3.9 years ago by zwdzwd120 • written 3.9 years ago by ankitplusplus30
1
gravatar for Benn
3.9 years ago by
Benn8.0k
Netherlands
Benn8.0k wrote:

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

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

ADD COMMENTlink written 3.9 years ago by Benn8.0k

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?

ADD REPLYlink written 3.2 years ago by pengchy420
1

Why don't you try enrichment first?

findMotifs.pl
ADD REPLYlink written 3.2 years ago by Benn8.0k

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.

ADD REPLYlink written 3.2 years ago by pengchy420
1
gravatar for zwdzwd
3.9 years ago by
zwdzwd120
zwdzwd120 wrote:

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.

ADD COMMENTlink written 3.9 years ago by zwdzwd120
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