We found that the expression patterns of several PD-implicated genes, identified in the two most recent genome-wide association studies7,8, were correlated with the Braak LB staging scheme. These included BRGs (SCARB2, ELOVL7, SH3GL2, SNCA, BAP1, and ZNF184; Table 1 and Supplementary Fig. 12) or genes present in Braak stage-related co-expression modules (GCH1, ITIH3, ITPKB, RAB7L1, BIN3, SATB1, ASHL1, MAPT, DLG2, and DNAH1; Fig. 3c).Table 1Braak stage-related genes that previously have been associated with Parkinson’s disease.Gene symbolEntrez IDCorrelation with Braak stages (r)P-value of correlation with Braak stages (BH-corrected)FC between R1 and R6P-value of FC between R1 and R6 (BH-corrected)Module memberReferenceSCARB2950−0.784.4e–04−1.441.7e–03M130Nalls et al.8ELOVL779993−0.677.2e–04−1.351.4e–03M84Chang et al.7SH3GL264560.704.5e–041.42.3e–03–Chang et al.7SNCA66220.703.3e–041.754.3e–04M3Nalls et al.8, Chang et al.7BAP183140.773.2e–031.991.6e–03M85Chang et al.7ZNF18477380.814.6e–042.342.9e–03M157Chang et al.7Several Parkinson’s disease variant-associated genes showed expression profiles that are correlated with Braak stages. The correlation r with Braak stages, fold-change (FC), and P-value of FC (t-test, BH-corrected) are within the selection thresholds for BRGs.
