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Yi, Andrew
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@yi-andrew-1165
Last seen 10.2 years ago
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
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