To identify genes with expression patterns that are associated with selective vulnerability to PD, i.e., BRGs, we correlated gene expression with the label of these vulnerable regions as defined by Braak stage. To ensure that genes have large expression differences across regions, we assessed differential expression between all pairs of Braak stage-related regions R1–R6, and found most significant changes between regions related to the most distant stages: R1 versus R5 and R1 versus R6 (|fold-change (FC)| > 1, Benjamini-Hochberg (BH)-corrected P < 0.05, t-test; Supplementary Fig. 2). Thus, in the selection of BRGs, we also focused on the FC between the disease-related end points R1 and R6.
