[BioC] Clustering and gene modules

[Sean Davis]

Why not look for differentially expressed genes between groups using Limma 
or some other package?  Then, characterize the sets of differentially 
expressed genes using gene ontology using a package like GOstats and 
GOHyperG?  This sounds like a more "traditional" analysis than what you are 
proposing.  Is there a reason not to look for statistically differentially 
expressed genes?

Sean

----- Original Message ----- 
From: "Min-Han Tan" <minhan.science at gmail.com>
To: <bioconductor at stat.math.ethz.ch>
Sent: Saturday, January 01, 2005 6:16 PM
Subject: [BioC] Clustering and gene modules


> New Year greetings to all.
>
> I have a problem which I am not sure how best to solve, and hope to
> seek advice from the list.
>
> I have 200 oligonucleotide arrays of about 13000 transcripts,
> belonging to approximately 6 different cancer subtypes. Essentially, I
> am hoping to first identify "gene modules" of gene expression
> corresponding to a specific cancer subtype, or groups of subtypes.
> (e.g. present only in A and B cancer, but not in C, D, E or F).
> Subsequently, I wish to label these modules by gene ontology. (e.g.
> "T-cell response" module)
>
> I tried a non-R program (GenXpress) which has been used to publish
> work in Nature Genetics, but I ran into quite a few freezes and
> glitches with the online cancer data posted alongside the program (not
> sure if it's a Windows issue on my side).
>
> I was thinking of first filtering the transcripts by variation and
> minimum expression, performing hierarchical clustering for the final
> gene set, choosing gene clusters by a minimum cluster size e.g. 20
> transcripts, sifting through these clusters to find "modules" by
> identifying subclusters differentiating between various permutations
> of cancer A, B, C, D, E and F to a minimum significance value, and
> then using the package gocluster to identify the relevant annotations
> for each of these clusters.
>
> Any advice would be greatly appreciated. Thank you!
>
> Regards,
> Min-Han Tan
> Van Andel Institute, MI
>
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