Questions about pathway analyses of genes with somatic mutations

alexbmp · 03-19-2012, 07:41 PM

Hi all

!!

I sequenced cancer exomes matched with normal exomes, then after alignment follwed by de-duplication, I extracted significant somatic mutations from the pile-up files with VarScan somatic option.

I want to ask if any of you can recommend me some decent pathway analyses, with "stringGene & integerSomaticMutation" as experimental input.
(Known pathways like KEGG or Reactome probably will be its database.)

I saw many gene-set (not essentially pathways) enrichment analyses,
with <phenotype of a sample>, <gene-expression-per-gene of a sample> as input (e.g. GSEA or Ingenuity),
but I haven't yet found a nice automated tool that gives you several significant candidate pathways when <gene:somatic-mutations> are given as input, not <gene:expression level>.

I think there are such tools out there; there is a high possibility I could not find them.

Have a joyful day!!

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03-19-2012, 07:41 PM	#1
alexbmp Member Location: Seoul, South Korea Join Date: Oct 2011 Posts: 30	Questions about pathway analyses of genes with somatic mutations Hi all !! I sequenced cancer exomes matched with normal exomes, then after alignment follwed by de-duplication, I extracted significant somatic mutations from the pile-up files with VarScan somatic option. I want to ask if any of you can recommend me some decent pathway analyses, with "stringGene & integerSomaticMutation" as experimental input. (Known pathways like KEGG or Reactome probably will be its database.) I saw many gene-set (not essentially pathways) enrichment analyses, with <phenotype of a sample>, <gene-expression-per-gene of a sample> as input (e.g. GSEA or Ingenuity), but I haven't yet found a nice automated tool that gives you several significant candidate pathways when <gene:somatic-mutations> are given as input, not <gene:expression level>. I think there are such tools out there; there is a high possibility I could not find them. Have a joyful day!!