to PPI network analysis, GeNets allows for gene set enrichment analysis on genes within the PPI network. We used Molecular Signatures Database (MSigDB) Curated Gene Sets (C2), curated from various sources such as online pathway databases, the biomedical literature, and knowledge of domain experts and Canonical Pathways (CP), curated from pathway databases such KEGG, BioCarta, and Reactome to test for gene set enrichment within the PPI network. Then a hypergeometric testing is applied to get P-value for gene set enrichment. We used Bonferroni-corrected P < 0.05 to correct for multiple hypothesis testing.
