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!!
!!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!!