[Bioc-devel] New Package - PGSEA - Parametric Gene Set Enrichment Analysis

Dykema, Karl Karl.Dykema at vai.org
Thu Dec 14 20:18:25 CET 2006

BioC developers,

Gene set enrichment analysis/categorical analysis is becoming a popular
method by which to examine gene expression data.  

While analysis of genes sets that are derived from canonical pathway
maps (KEGG, GO, etc) can be informative, it is also informative to
examine gene lists that are deregulated in response to a defined
experimental procedure (application of drug, gene knock-down, etc).
These genes lists can be collected from the literature or re-derived
from data deposited in gene expression databases. 

We have put together a small package in an attempt to codify this idea.
The package is similar to the Category package that already exists, but
tries to de-couple the complexities of collecting and annotating gene
lists from the specific categorical analysis method. Included in this
package is a small collection of signatures were collected from various
articles. In addition, we have included a set of signatures derived from
the dataset published by Lamb et al., in the paper "The Connectivity
Map: using gene-expression signatures to connect small molecules, genes,
and disease." 

Is there an existing effort and/or any interest in setting up a
structure to curate and exchange experimental derived gene lists within
BioC? I know that other groups are working on collecting databases of
such signatures and am on the fence about how much to invest in this
effort.  Any feedback would be welcome.



Karl Dykema
Laboratory of Computational Biology
Van Andel Research Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503 
(616) 234-5554
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