Extracting gene subnetwork from pathways using gene expression data

Question

[Nicolas Rosewick]

Hi,

I've a bunch of RNA-Seq data (treated vs untreated) and I want to map these expression data (analyzed with DESeq2) on known biological pathway such as KEGG or Reactome. and to extract subnetwork enriched in differentially expressed genes. Anyone knows good recent publications about this type of analysis ; or any advice to how to start the analysis: tools? Which pathway format (sif? biopax?)

Thank you

Answer 1

[andrew]

One of our collaborators published on this in2013. You can read the abstract and link to the paper from the science section of our website here.

Analysis and correction of crosstalk effects in pathway analysis.