We generated brain region-specific co-regulation networks based on the RNA-seq data from 8,544 samples (Supplementary Note and Supplementary Figs. 31–33) using a similar approach to our previously developed multi-tissue GeneNetwork (n = 31,499)54,55. We applied Downstreamer56 to SCZ57, PD58, MS29, AD59 and amyotrophic lateral sclerosis (ALS) GWAS summary statistics60, using these networks to prioritize genes that are co-regulated with genes in their GWAS loci (Supplementary Note, Supplementary Fig. 34 and Supplementary Tables 25–30). For MS and AD, these were mostly immunity genes, whereas for PD, ALS and SCZ, these were genes that are specifically expressed in the brain (Supplementary Tables 25–30). For ALS and MS, we additionally created smaller networks for the cerebellum (n = 715) and cortex (n = 6,526) to identify brain region-specific effects.
