how to compare promoter regions from two genes - (Oct/03/2007 )
I am new to bioinformatics and I am hoping someone can help me with this. I have an a gene (DNMT1) which has been shown to mediate expression of certain genes by modifiying their promoters (ie methylation). Currently, I have a list of genes (aquired from gene array study) that I believe may also be mediated by DNMT1. What I like to do is to compare promoter regions of known targets of DNMT1 (eg. cdc2) with promoter regions of the genes in my list in such a way that it could tell me whether or not the gene being compared has the possibility of being mediated by DNMT1? For the sake of clarity here is an artificial example of what I would like to do.
Say I have a list of genes I think could be potential targets for DNMT1 (jak1 and jak2). I find that DNMT1 can mediate expression of cdc2 by methylation in pubmed. I then do some kind of bioinformatic search and find that cdc2 promoter is similiar to the promoter region of jak1 and thus giving me a clue that DNMT1 could be mediating jak1 as well. What I want to know is how to perform this comparison.
Hopefully this makes sense to anyone that is reading this.
May be this could be helpful
Finding some sequence elements that may dictate DNA methylation has been tried by many people and also by myself. The effort has been largely unsuccessful. You could use the MEME program to find short motif shared by different sequence. the program can be found here http://meme.nbcr.net/meme/intro.html. You need to compile different promoter sequences into a FASTA file and analyze this file using MEME. Or you can the free Vector NTI program from Invitrogen to do a mutliple sequence alignment to see if there are short consensus sequences.