Linking Transcription Factors To Gene Promoters

Question

[Eric]

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.

[Obi Griffith]

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

Answer 1

[Anthony Mathelier]

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.

Answer 2

[Obi Griffith]

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.

Answer 3

[Martombo]

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.

Answer 4

[Charles Warden]

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

Answer 5

[jin]

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.