[Bioc-devel] A geneSet data class for facilitating GSEA

Dear bioc-developers,

would it be useful to introduce an additional slot for the direction and/or
magnitude of expression change of each gene in the gene set?

It seems that GSEA and GSEA-like methods use sets of genes that are
homogeneously down- or upregulated (correct me if I am wrong, I am far from
being up to date on GSEA methods).

This seems to be reflected in the example presented in the PGSEA vignette
where target genes of Ras and Myc are separated into 'UP' and 'DN' regulated
genes. 

However, (alternative?) methods could actually use the quantitative
information about expression changes to score each gene set. Adding a
corresponding slot in the geneSet class would allow to accommodate such
methods.

Best,
Alexandre


-----Original Message-----
From: bioc-devel-bounces at stat.math.ethz.ch
[mailto:bioc-devel-bounces at stat.math.ethz.ch] On Behalf Of Dykema, Karl
Sent: mercredi, 14. mars 2007 16:15
To: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] A geneSet data class for facilitating GSEA

Sorry I forgot to attach the str()

$ 15-delta prostaglandin J2 10 uM  DOWN : list()
  ..- attr(*, "reference")= chr "15-delta prostaglandin J2 10 uM  DOWN "
  ..- attr(*, "desc")= chr "DOWN "
  ..- attr(*, "source")= chr "PubMed"
  ..- attr(*, "design")= chr "????"
  ..- attr(*, "identifier")= chr "17008526"
  ..- attr(*, "species")= chr "human"
  ..- attr(*, "data")= chr "raw"
  ..- attr(*, "private")= chr "no"
  ..- attr(*, "creator")= chr "Karl Dykema <karl.dykema at vai.org>"
  ..- attr(*, "ids")= chr [1:75] "171392" "5680" "2149" "54557" ...
  ..- attr(*, "class")= atomic [1:1] smc
  .. ..- attr(*, "package")= chr "PGSEA"


This closely mirrors the geneSet proposed and we will be happy to adopt
a consensus structure.

The only significant difference is a "creator" to let folk know who
curated the gene list... This may help if groups are collaborating to
the collect gene sets.


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



-----Original Message-----
From: Vincent Carey 525-2265 <stvjc at channing.harvard.edu>
Date: Wed, 14 Mar 2007 10:19:36 -0400 (EDT)
To: Sean Davis <sdavis2 at mail.nih.gov>
Cc: <bioc-devel at stat.math.ethz.ch>, Ross Lazarus
<rerla at channing.harvard.edu>
Subject: Re: [Bioc-devel] A geneSet data class for facilitating GSEA

i like this idea in principle.  the RGenetics folks may have done
something in this direction.

you might want to have geneList as an abstract class, and then extend to
EntrezGeneList, RefseqGeneList and so forth so that dispatch could work
without looking into the idType ...

a version or date field might also be important

---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

GSEA, both the specific method and the general concept, is becoming 
more prevalent and important in data analysis.  There have been 
several mentions of including various "gene lists" for use with 
Category or other methods.  Is there interest in making a generic 
geneSet class for storing such information?  (Or does it already exist

and I just haven't seen it?)  I bring this up because I think it could

be quite useful to have a general solution for the community (like the

eSet class has become).  A class could be as simple as a vector of 
Entrez Gene IDs to something more complicated (but perhaps a bit more

useful for general consumption) like:

identifier: an identifier for the set (perhaps from a public database 
like
MSigDB)
title:  One line title
description: free text description
species: The species to which the dataset applies
URL: from where the data were derived
MIAME: class "MIAME" object
protocol: (could be in MIAME, also) description of methods to produce 
genelist from raw data source
idType:  What type of ID is stored (Entrez, Refseq, Ensembl, etc)?
geneList: vector of IDs

A simple wrapper data structure (even just a list) could then be used 
to distribute the geneSets.  Some methods could then be defined for 
converting to an incidence matrix for use by Category, etc.  But I 
think the most important points from above are 1) maintaining some 
metadata about the genelists and 2) standardization to reduce 
duplicated work.  Individual groups would then instantiate the 
geneSets using whatever means they see fit (parsing MSigDB, IPI files,

etc.).

Any thoughts?

Sean

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