PSEN1 and Alzheimer disease: We observed the highest enrichment significance in module 1 (M1) which was amyloid-β metabolism (top GO process: q = 5.3E-05, Table S8), including the Alzheimer’s disease (AD) relevant genes: APP, PSEN1, CLU, ROCK2 and DYRK1. The central role of APP was confirmed by a separate protein-protein interaction analysis showing this gene as the most important hub in a network that included 30% of the DEGs generated using WEBGESTALT [75] (Fig. S9).