transcription factor binding consensus sequence download

Question

[ravihansa82]

Dear friends

I need to compare TFs bind with set of human genes promoters and relevant first introns So I need to find out transcription factors and consensus sequence/s of their binding sites. I went through some data bases,such as -oreganno (which is not up dated to date,but having set of sequences and their consensus)...considering more reliable database, I went through JASPER.. but I could not download all consensus sequence of human TFs. Similarly I went through MotifMap database also it also having consensus but i could not download them..

So I need help to do that..........

Thank you

Answer 1

[Alex Reynolds]

Maybe some have precalculated results, but these steps seems highly dependent on the parameters of your experiment and the annotations you want to work with, so you may have to do some things manually.

For instance, given PWMs from sources like JASPAR, TRANSFAC, UniPROBE, Taipale, etc. you could use a tool like FIMO or matrix-scan to calculate putative TF binding sites.

Once you have the sites, you can retrieve the sequences via UCSC Genome Browser or other query tools.

Once you have the sequences, you can run them through a tool like Weblogo to generate sequence logos, consensus sequences, etc.

[ravihansa82]

Thank you very much Alex. actually i need to do the following task. I have about set genes and I downloaded appropriate promoter and first intron sequence for every gene. I need to find out functional significance of first intron.So I though to compare and contrast, how the promoters and the first intron interact with known set of TFs. in this case I need to compare how much both promoter and first intron share TFBS. that is why I thought to get the consensus sequence of TFBS and do the comparison...

I downloded Motis sites from JASPER. but such sequences also having some other sequence segments along with consensus sequence. then I found some TFs and binding site from http://genome.crg.es/datasets/abs2005/data/abs.gff. OregAnno database also having TFBS but it is not updated...MotifMap alos having but difficult to get the sequences...in PASAR .. I have to go TF by TF factor to get sequences....

Actually I did not understand what you meant to obtain by interest seq along with PWM..

Can I get suggestions....