Hi All I have 5 TFBS (predicted by Pscan software on promoters related to 7 over-expression genes in adipose tissue) that i want to find other genes which has all of the TFBS. in other words, i want to find another genes with same promoter profile with 7 over-expression genes. I couldnt find such software or web-server and some thing like this to do my works. i need a tool which search my TFBS on a set of promoters and bring me genes with same promoter profile. thanks a lot in advance regards
One option is using MAST from MEME suite. This is not the ideal tool but you can choose the upstream region of all the human genes (you can't set the length of the upstream region) and then convert your promoters to MEME format which can be done using some excel manipulations and text editing. This solution is not ideal but at least you will get a graphical view of the binding sites of the different TF.
It's been a long time since I used it but Genomatix does something very similar to this and if you haven't used it before, you get a weeks free trial I think. It gives you nice pictures of the binding sites as well allong the promoters of the genes.
I'm not sure if you are looking for software to search for matches to motifs, or something more elaborate. There are several tools available for searching for matches to motifs:
Regulatory Sequence Analysis Tools (RSAT). In particular take a look at their 'matrix-scan' tool.
I'm sure there are others.
You can try using the INSECT's server.. it allows the search of TFBS on a list of genes from ensemble relative to their TSS. And you can add up to 5 TFBS putting also restrictions among their to perform the search. You can find the description of the method here http://www.ncbi.nlm.nih.gov/pubmed/24008418.You will only need the IDs for all the human genes from Ensembl and voila,