We validated whether the identification of BRGs was confounded by variations in cellular compositions across the six Braak stage-related regions R1–R6. We applied population-specific expression analysis (PSEA)24 to the AHBA to validate the cell-type specificity of each of the 960 BRGs. We found all 960 BRGs to be differentially expressed (BH-corrected P < 0.05, t-test) between regions R1 and R6 after correcting for five major cell-types (neurons, astrocytes, oligodendrocytes, microglia, and endothelial cells). For example, the neuronal marker ADCY1 which was identified as a BRG remains differentially expressed between regions R1 and R6 when corrected for neurons or other cell-types (Fig. 4). Similarly as for BRGs, PSEA analysis on all 23 Braak stage-related co-expression modules showed significant differential expression between regions R1 and R6 which cannot be fully explained by differences in cellular composition.
