I want to check whether any response element is present for a particular set of transcription factors on my gene of interest. I have already found EPD (http://epd.epfl.ch/) for promoter sequence and motif search and JASPAR (http://jaspar.genereg.net/) for response sequences. But the problem is, I am not able to merge those information.
The problem with EPD is, many gene promoters are not available. Even if they are available and I find transcription factor motifs on my gene of interest, there is no way to see them as sequence and annotate it.
So, if someone knows any software/ database/ technique for this purpose, it will be immensely helpful for me.
Have you tried looking at the UCSC Genome Browser? Have a look through the different annotation tracks. Depending on the organism, they often have both experimentally identified and in silico predictions of various regulatory elements. JASPAR even has links to UCSC browser tracks for their data.
Ryan
Hi Biswajit Biswas
in addition to the good advice from Ryan Michael Spengler , I'll say that if it's for human, go to the genome browser (http://genome-euro.ucsc.edu/cgi-bin/hgGateway?redirect=manual&source=genome.ucsc.edu) with the hg19 build and see your genes with the "TFBS conserved" optional track.
if you have too many genes to check and prefer see a file, go to the table browser and search for this track with the defined regions of your genes.
fred
Thanks Ryan Michael Spengler and Frederic Lepretre , I will try it and will post the result.
Thanks a lot for responding.
Hello Frederic Lepretre ,
Sorry to disturb you again. I tried to do what you said, and tried adding "TFBS conserved" optional track, but it didn't work, don't know why. And it is only available hg19 build and not the latest build, and that too for human genes because I didn't find any such tracks for mouse assemblies.
Hi Biswajit Biswas ,
lot of optional tracks are released for hg19, since hg38 is a temporary build. zooming out of your gene to get 10-20kb sequences more on 5' could help you, I hope, to see TF (turn the TFBS option to pack). if you don't manage, just send me a private message, I'll help you.
fred
Biswajit Biswas I'd also recommend looking at the various ENCODE tracks. For example: https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=725021383_RGLKNnOIuYWhC8gnLaWXEWCGidL3&c=chr21&g=wgEncodeTfBindingSuper gives you actual TFBS data from experiments. You can click on the names of any track to see detailed information. Keep clicking through the links on the subsequent pages to turn on/off specific TFs and cell lines.
For mouse, there are several experimental TFBS tracks in the mm9 assembly under "Expression and Regulation".
As Frederic Lepretre pointed out, the table browser option will allow you to pull the associated information for your genes/regions of interest. I'd also be happy to help further by private message, if you need it.
Good luck,
Ryan
You can also scan your promoter sequence with the TF motifs of interest with the FIMO tool from the MEME suite (http://meme-suite.org/).
Good luck !
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