In the PD microarray dataset, samples were collected from the medulla oblongata (R1), locus coeruleus (R2), and substantia nigra (R3) from PD patients (67.6% males, mean age 78, range 61–87 years), iLBD patients (42.4% males, mean age 80, range 56–98 years), and non-demented controls (54.5% males, mean age 77, range 60–91 years) (Supplementary Table 2 and Supplementary Data 4). The PD microarray data of the substantia nigra (R3) was previously published in Dijkstra et al.11 (GEO accession number GSE49036). Based on pathological examination, PD patients in the microarray dataset revealed LB pathology in accordance with Braak stages 4–6, and iLBD patients showed LB pathology in the brainstem (Braak stages 1–3), and therefore represent the early stages of PD. Additional samples from the medulla oblongata (R1) and locus coeruleus (R2) were collected and processed of the same cohort in the same manner for hybridization on GeneChip® Human Genome U 133 Plus 2.0 arrays. Probe IDs were mapped to Entrez IDs with the mapIds-function in the hgu133plus2.db R-package v3.2.3. We removed 10,324 out of 54,675 probes with missing Entrez IDs. The remaining
