In conclusion, we identified genes and pathways that may be important to maintain biological processes in specific brain regions, but may also contribute to a higher selective vulnerability to PD. Our results suggest that interactions between microglial genes and genes involved in dopamine synthesis and motor functions, as well as between genes involved in blood-oxygen transport and the immune system may contribute to the early involvement of specific brain regions in PD progression. Our observations highlight a potential complex interplay of pathways in healthy brains and provide clues for future genetic targets concerning the pathobiology in PD brains.