I'm not aware of a compiled database of BioCarta pathways, but for me
the quickest way to get the genes from a pathway of interest is as
follows:

- Use http://cgap.nci.nih.gov/Pathways/BioCarta_Pathways in stead of the
BioCarta site
- Select pathway
- Click 'Genes' link
- Click '[Text]' link
This page contains tab-separated ids of the genes in the pathway with a
choice of Symbol, Title, Genbank accession, Unigene, and
LocusLink/EntrezGene

These should prove quite simple to connect to your dataset


The GSEA gene sets
http://www.broad.mit.edu/gsea/msigdb/msigdb_index.html contain a number
of BioCarta pathways, but unless you use one of the platforms supported
by GSEA it may prove hard to connect these to your dataset.

If you are working in Windows I can provide you with a tool that makes
using the globaltest easier with regards to selecting genelists, and
working with KEGG and GO

In an attempt to start the discussion on your first question about
testing with low numbers of replicates let me state my feelings as a
non-statistician about them.
List methods (testing whether proportion of differentially expressed
(DE) genes in a pathway is increased through Fisher exact or
Chi-square):  this probably depends on the way the DE list was
determined. By using a method that performs well with small groups like
Limma you should be fine

GSEA determines whether the genes of a pathway are ordered non-randomly
in a ranked list of genes according to DE. This could also be a list
produced by Limma

The global test uses the expression information of all genes in the
pathway to determine whether groups are different with regard to the
pathway. Although the expression of different genes within a sample is
not at all independent, I think this will still help you in a situation
with a low number of replicates.

To conclude: I don't have a clue which method has the highest power in
your situation, but I hope someone else can shed a light on it

Jan 



-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Anthony Bosco
Sent: Mon 10-Jul-06 6:14 AM
To: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] Gene set analysis/Global test with 3 replicates
 
Hi,

I would like to perform gene set analysis using global test or 
another method (suggestions?) but I only have 3 biological replicates 
for each condition and I am not sure which method is the most 
powerful to use in this case.

Also, has anyone compiled Biocarta pathways into gene lists for gene 
set analysis.


regards


Anthony

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