Expression patterns of Braak stage-related genes (BRGs) across brain regions of non-neurological, incidental Lewy body disease (iLBD) and Parkinson’s disease (PD) brains.a Selection of BRGs that were either negatively (blue; r < 0) or positively (red; r > 0) correlated with Braak stages. Genes were selected based on (1) highest absolute correlation (|r|) of gene expression and Braak stage labels, (2) highest absolute fold-change (FC) between R1 and R6, and (3) lowest P-value of FC in the differential expression analysis (BH-corrected PFC), for which the top 10% (2001) genes resulted in the shown thresholds. The overlap between the three sets of top 10% genes resulted in 960 BRGs. b Correlation r of BRGs (red and blue points) with Braak stages (x-axis) and –log10 BH-corrected P-value (y-axis). c Mean expression of BRGs for each region (colors) and donor (opacity) in the AHBA (number of samples in Supplementary Table 1). d Validation across 134 non-neurological individuals in UK Brain Expression Consortium (UKBEC; R1: medulla, R3: substantia nigra, R5: temporal cortex, R6: frontal cortex), and e 88–129 non-neurological individuals in Genotype-Tissue Expression Consortium (GTEx; R3: substantia nigra, R4: amygdala, R5: anterior cingulate cortex, R6: frontal cortex). Each data point is a sample with the mean expression of negatively or positively correlated BRGs. f Validation in PD microarray dataset (R1: medulla oblongata, R2: locus coeruleus, R3: substantia nigra; number of samples in Supplementary Table 2) and g PD RNA-seq dataset (R3: substantia nigra, R4/R5: medial temporal gyrus; number of samples in Supplementary Table 3). Boxplots (f, g) are shown per patient group (PD, iLBD, and control) and per brain region (Supplementary Fig. 5). The boxplots indicate the median and interquartile range (25th and 75th percentiles) with whiskers indicating 1.5 times the interquartile range; outliers beyond the whiskers are plotted individually.
