I can modify the question... Where can I find a complete list of all gene expressed in the brain... From that, I have a good idea of what to do. Simon No?l CdeC ________________________________________ De : Steve Lianoglou [mailinglist.honeypot at gmail.com] Date d'envoi : 13 mai 2011 17:10 ? : Simon No?l Cc : bioconductor at stat.math.ethz.ch Objet : Re: [BioC] How to filter a list of SNPs? Hi, 2011/5/13 Simon No?l <simon.noel.2 at="" ulaval.ca="">: > > Hello every one. I have a really big list of SNPs from all the genome and > I want to restrict that llist to SNPs that point to gene expressed in the > brain. How should I procede and with wich package? To help you get better answers, can you explain what you mean by a SNP "point[ing] to" an expressed gene? Here's an answer to a question you *might* be asking: If you are talking about filtering your SNP list to the SNPs that are in cis to genes that are expressed, I would: (1) Get the appropriate gene expression data so you can get a list of expressed genes (2) Use GenomicFeatures to build a TranscriptDb using your gene annotations of your choice (3) extend the transcripts from (2) by some (cis) distance you determine is appropriate and store in `extended.expressed.genes` (4) store your SNPs as a GRanges object (I guess set strand to "*") named `snps` (5) shorter.snp.list <- subsetByOverlaps(snps, extended.expressed.genes) (6) ... (7) publish -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact