To examine gene expression patterns across brain regions involved in PD, we used normalized gene expression data from the AHBA15, a human post-mortem microarray dataset of 3702 anatomical brain regions from six non-neurological individuals (five males and one female, mean age 42, range 24–57 years). We downloaded the data from http://human.brain-map.org/. To filter and map probes to genes, the data were concatenated across the six donors. We removed 10,521 probes with missing Entrez IDs, and 6,068 probes with low presence as they were expressed above background in <1% of samples (PA-call containing presence/absence flag15). The remaining 44,072 probes were mapped to 20,017 genes with unique Entrez IDs using the collapseRows-function in R-package WGCNA v1.64.146 as follows: (i) if there is one probe, that one probe is chosen, (ii) if there are two probes, the one with maximum variance across all samples is chosen (method = maxRowVariance), (iii) if there are more than two probes, the probe with the highest connectivity (summed adjacency) is chosen (connectivityBasedCollapsing = TRUE). Based on the anatomical labels given in the AHBA, 2334 out of 3702
