Question: Detecting overrepresented genomic loci
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gravatar for Yi, Andrew
14.6 years ago by
Yi, Andrew20
Yi, Andrew20 wrote:
You can try DigMap system can detect differential regions based on either expression array or CGH array http://160.129.212.234/digmap/ http://geneexplorer.mc.vanderbilt.edu/digmap/ Andrew -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Sean Davis Sent: Tuesday, March 29, 2005 3:15 PM To: jeffrey rasmussen Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Detecting overrepresented genomic loci You might look at GLAD, DNAcopy, and aCGH as possibilities, but this isn't exactly what you want, I suppose given that you have a set of differentially expressed genes already. Another tact is to look at something like WebGestalt (online tool). It allows you to give a set of genes as input and can plot where these genes are on the genome. Finally, you could use something like Fisher exact test by region or chromosome arm to determine the "significance" of clustering by region but this would require some coding on your part. Sean On Mar 29, 2005, at 4:07 PM, jeffrey rasmussen wrote: > Hi all, > > My goal is to discover regions with multiple adjacent genes > coordinately regulated. Are there any packages that would allow one to > test for genomic loci that are overrepresented in a subset of genes > versus the remaining genes on the chip? I have tried using the > geneplotter package to visualize the genomic distribution of > differentially expressed genes, however, I have found it difficult to > identify candidate loci from these plots because neighboring genes are > indistinguishable from each other on the output graphic. > > Thanks, > Jeff. > > __________________________________ > Jeffrey Rasmussen > Research Consultant, Bioinformatics > Department of Immunology > University of Washington > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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