In GSEA software, the Affymetrix HG-U133A 2.0 transcript IDs of all nominally differentially expressed (p≤ 0.05) mRNA transcripts were converted to HUGO Gene Nomenclature Committee (HGNC) gene symbols and in cases of multiple transcripts representing a single gene, the probeset with the highest MM was retained [97]. A priori gene sets were obtained from the Molecular Signatures Database v4.0 (MSigDB; http://www.broadinstitute.org/gsea/msigdb) from the Broad Institute. A total of 1320 gene sets from the Canonical Pathways subset of the C2: Curated Pathways collection of MSigDB was assessed. Default parameters were then applied to give a minimum and maximum a priori gene set size between 15 and 500 genes, respectively. Of the 1320 a priori gene sets used for GSEA from the C2: Curated Pathways collection from MSigDB, 929 gene sets were excluded due to gene set size parameters (i.e. gene sets smaller than 15 genes) and 391 a priori gene sets were used for final GSEA analysis.
