I am working to find out which transcription factors (TFs) may binding to my target gene’s promoter to regulate its expression. In the past, I used the ConSIte web site to find the potential TFs in a genes promoter, but I don't think this website was satisfying.
You can start trying out these web tools: http://www.protocol-online.org/prot/Research_Tools/Online_Tools/Sequence_Analysis/Transcriptional_Factor_Binding_Site_Search/
Specifically for plants, I would add PLACE: http://www.dna.affrc.go.jp/PLACE/
Have a look on this site: http://www.usc.edu/hsc/nml/lib-services/bioinformatics/promoter_TF.html
Unfortunately TESS seems to be offline now (although you can still get the code). Would be cool if someone could set up a web service again, since this was a pretty useful tool.
If you know your Transcription factor consensus sequence, you can search tthrough promoters using RSAT: http://rsat.ulb.ac.be/rsat/
Hi,
You can try TFSEARCH here is the link (http://www.cbrc.jp/research/db/TFSEARCH.html). We use this TFSEARCH in our lab.
BYe
Thank all of you!
And I have another question about these predictions. After the analysis you can get a list of the TF binding sites, it sometimes includes both the plus and minus strands. Does that matter? Should we take the orientation for consideration?
I also use Opossum (http://burgundy.cmmt.ubc.ca/oPOSSUM/). A number of predicted binding sites is an important indicator of actual potential binding (and a regulatory role) of a TF. Using the co-expressed or orthologous genes in comparative analysis also enhances the reliability of prediction of the binding sites. Plus/minus or both strands binding sites requirements are different for different types of TFs.
TRANSFAC by BioBase is very good, but after the trial period it is not free. This business of 'privatizing' these softwares is somewhat depressing !!
@Prem Subramaniam: I understand your frustration, however, please consider that without this kind of 'privatization', TRANSFAC would have disappeared about 15 years ago because of lack of 'public' funding. Some people accepted considerable personal (including financial) risk to maintain that resource with private money. The people working on TRANSFAC every day earn money, which has to come from somewhere. It is always the same: somebody has to pay the bill. When it is from public funding, it is the tax payers. Here, it is the user community. Although it imposes some inconvenience for the users, I don't think it is unfair to let those pay who actually need such a resource.
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