The PD Braak staging scheme defines a temporal order of brain regions affected during the progression of the disease18. Based on the sequence of events as postulated by Braak et al.1, we hypothesized that genes whose expression patterns increase or decrease across regions involved in the Braak staging scheme might contribute to higher vulnerability to LBs in PD brains (Fig. 1). Based on this assumption, we aimed to find (1) which genes are involved, (2) which modules of interacting genes are involved, and (3) which biological processes contribute to this vulnerability. We analyzed the regions of interest using a microarray dataset of anatomical brain regions from six individuals without any known neuropsychiatric or neurological background from the AHBA15. Therefore, we first assigned 2334 out of 3702 brain samples to Braak stage-related regions R1–R618: myelencephalon (medulla, R1), pontine tegmentum including locus coeruleus (R2), substantia nigra, basal nucleus of Meynert, CA2 of hippocampus (R3), amygdala, occipito-temporal gyrus (R4), cingulate gyrus, temporal lobe (R5), frontal lobe including the olfactory area, and parietal lobe (R6) (Supplementary Table 1, and Supplementary Fig. 1).
