I am looking for a web interface where I can get a genome-wide prediction of target genes for a define transcription factor binding site. Just the raw prediction not filtered for any functional meaning or cell type biaised (so I am not interested in ChIP validated data.
Check this sites, hope you find something that suits you!
https://www.genomatix.de/online_help/help_matinspector/matinspector_help.html
http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3
http://linux1.softberry.com/berry.phtml
http://www.gene-regulation.com/pub/programs.html
There are a number of sites that can help with this (as listed above) and it might be a good idea to do some comparison to test for congruence. There are so many microenvironmental factors and network interactions influencing transcription that genome-wide interpretations should be handled carefully.
You can try using MatInspector. MatInspector is a software tool that utilizes a large library of matrix descriptions for transcription factor binding sites to locate matches in DNA sequences.
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