Overlap of pathways. Number of enriched pathways that overlap between two comparable datasets (hippocampal field CA1 region for patients with severe AD), using four different methods (i.e., PathNet: the present study, SPIA: signaling pathway impact analysis, GSEA: gene set enrichment analysis, and the hypergeometric test). As an example, PathNet identified 22 and 17 statistically significant pathways from the brain regions dataset and the disease progression dataset, respectively. Ten of these pathways overlapped. The statistical significances of the overlaps from each of the four methods were tested using the hypergeometric test; p-values were as follows: pPathNet = 2.0 × 10-5, pSPIA = 1.5 × 10-4, pGSEA = 1.0, phypergeometric = 3.3 × 10-4.