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.
Thanks.
