I used to run these querries at:
- http://genecodis.dacya.ucm.es/analysis/ (you can use Transcription factors only for this appplication)
- http://atted.jp/ (finds coregulated genes, you can use the output to feed the former tools)
I am sure there are other sites all based on some adapatation of the UCSC conserved TFBS track
to go deeper and across species for a given region, use * http://bioit.dmbr.ugent.be/ConTra/index.php *... google it
these web-tools ar eeasy and give you results you of course will need to validate.
Hello, I would suggest you the PSWM usage. You could download the matrices of the TFs, and use them to predict TFBS among the genes of the list. For known targets I would suggest iHOP, a tool capable of retrieving literature-based information about several genes.