The following pathways were deregulated in SN tissue of PD patients with Braak alpha-synuclein stage 5–6 (BH-FDR<0.05) and have been previously described by others [19, 22, 24, 25, 28, 30, 33]: PI3K/AKT signaling (BH-FDR = 0.00032), PTEN signaling (BH-FDR = 0.00096), B cell receptor signaling (BH-FDR = 0.0019), mTOR signaling (BH-FDR = 0.0053), dopamine receptor signaling (BH-FDR = 0.03), ephrin receptor signaling (BH-FDR = 0.03), Huntington’s disease signaling (BH-FDR = 0.02), and axonal guidance signaling (BH-FDR = 0.02). Here, MTOR is linked to juvenile Huntington disease.