We selected 23 co-expression modules for which the eigengene was significantly correlated with Braak stages (BH-corrected P < 0.0001, t-test). These modules have distinct expression patterns (Supplementary Fig. 8) and those that were negatively correlated with Braak stages showed more distinct expression patterns than the positively correlated modules (Supplementary Fig. 9). Module M39 showed the lowest correlation with Braak stages (r = −0.87, BH-corrected P = 3.65e–7, t-test), while M50 showed the highest correlation (r = 0.92, BH-corrected P = 4.42e–7, t-test). Most modules were significantly enriched for BRGs that were similarly correlated with Braak stages (BH-corrected P < 0.05, hypergeometric test; Fig. 3c). For functional characterization, modules were further assessed for enrichment of cell-type markers23, and gene sets associated with functional GO-terms or diseases. A full version of the table in Fig. 3c showing all significant associations is given in Supplementary Fig. 10.
