[BioC] Detecting overrepresented genomic loci

Yi, Andrew andrew.yi at Vanderbilt.Edu
Tue Mar 29 23:26:51 CEST 2005

You can try
DigMap system can detect differential regions based on either expression
array or CGH array


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis
Sent: Tuesday, March 29, 2005 3:15 PM
To: jeffrey rasmussen
Cc: bioconductor at 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.


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
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> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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