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Old 03-19-2012, 06:41 PM   #1
alexbmp
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Location: Seoul, South Korea

Join Date: Oct 2011
Posts: 30
Smile 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!!
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cancer exome, cancer genome, exome sequencing, pathway analysis, somatic mutation

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