How to analyze regulator domain at promoter region - (Feb/16/2006 )

Hey.

Thanks to this forum, I am working on a gene which is methylated at the promoter region.
I fellowed the post which pcrman gave, i.e. find the promoter sequence at Ensemble site, then fed in the methprimer software.
After it showed it is methylated, I like to see what domains are in the promoter region, like NF-kB, AP1, sp1, etc. binding sites.
I found one web site
http://bimas.dcrt.nih.gov/molbio/signal/
it seems may do the job. but it gave so many binding sites that i kind of doubt if that is what I really want.

can someone help me with this?
Thanks!

such a site is great for predicting promoter binding sites, but you may need to perform a biochemical footprinting analysis to determine exactly if and where the transcription factors are binding to your promoter.

Usually with CpG islands there will be lots of TF binding sites, and as not all TF's have been characterised, there maybe many more. Unless you know which one binds to your promoter then it's a matter of elimination then.

Nick

Thanks for your reply, Nick.

It shounds very complicated now, I heard footprinting is very diffcult(never did it).
There is no other easy way out?