Question: Linking Transcription Factors To Gene Promoters
3
gravatar for Eric
6.6 years ago by
Eric90
Eric90 wrote:

Hello,

I have a single gene and I would like to predict which transcription factor acts on its promoter. Any clue how to go about that would be appreciated.

Thanks.

• 2.0k views
ADD COMMENTlink modified 2.4 years ago by jin80 • written 6.6 years ago by Eric90

You have a single __? Gene I presume? Please edit to make your question complete.

ADD REPLYlink written 6.6 years ago by Obi Griffith17k
2
gravatar for Anthony Mathelier
6.6 years ago by
University of Oslo, Oslo, Norway
Anthony Mathelier870 wrote:

Hi,

You could use PWMs from the JASPAR database and apply them to your promoter region (restricting your analysis to conserved regions will reinforce the predictions). To do so, you can use the ORCAtk website at http://cisreg.cmmt.ubc.ca/cgi-bin/ORCAtk/orca

Feel free to ask if you have any further question.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Anthony Mathelier870
0
gravatar for Obi Griffith
6.6 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

I suggest CONSITE. Select the "Analyze single sequence" option. Enter the promoter sequence for your gene of interest and (optionally) the cDNA sequence. In the next step you may want to select only TFs for your species of interest. After you hit the 'Analyze...' button, I like to look at the sequence view.

ADD COMMENTlink written 6.6 years ago by Obi Griffith17k
0
gravatar for Martombo
5.1 years ago by
Martombo2.4k
Seville, ES
Martombo2.4k wrote:

try with SwissRegulon: http://swissregulon.unibas.ch/fcgi/sr/swissregulon

it is based on phylogenetic conservation, ChIP data and annotation of binding sites from the literature. you can look up for a gene and you get directly to its promoter region. then you can download the data about TFBS.

ADD COMMENTlink written 5.1 years ago by Martombo2.4k
0
gravatar for Charles Warden
5.1 years ago by
Charles Warden6.4k
Duarte, CA
Charles Warden6.4k wrote:

You can search for transcription factors in promoter sequences (at your desired confidence interval) via gene symbol using TRED:

http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm

ADD COMMENTlink written 5.1 years ago by Charles Warden6.4k
0
gravatar for jin
2.4 years ago by
jin80
jin80 wrote:

For plants, you can try PlantRegMap, which predicts TF binding sites based on sets of manually curated, non-redundant, high-quality TF binding motifs derived from experiments.

ADD COMMENTlink written 2.4 years ago by jin80
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