Question: How to do pathway analysis on kinome Drosophila dataset
gravatar for m98
11 months ago by
m98280 wrote:

I am familiar with gene set enrichment analysis (GSEA - Broad Institute) using sequencing data but I am fairly unexperienced in pathway and/or GO analysis in other contexts. My questions are:

  • Is it possible at all to perform gene set enrichment/pathway analysis/GO analysis on data from a drosophila siRNA kinome screen ? In this context, I have a file with a 2 columns: a gene name and a score from the screen (the score reflects kinase activity).

  • If so, is there a minimum "sample" size (i.e number of genes in this case) required to do this analysis? When doing this on RNAseq data, you would have thousands and thousands of genes. Here, I have around 500 genes. Do I even have any statistical power to do this kind of analysis? I'm not sure where to find this information.

  • What packages are available for such analyses? It unclear to me whether GSEA (Broad Institute) is suitable - i.e. gene set enrichment analysis might not be suitable, perhaps I should do a "simpler" KEGG or GO analysis with another software (DAVID, Panther etc?) I would appreciate any software recommendation as I am a bit confused by the many software available.


ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 11 months ago by m98280
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