dataset, SNCA was significantly lower expressed in the substantia nigra (R3) compared to the medial temporal gyrus (R4/R5) in PD patients, but again not in controls (BH-corrected P < 0.05, DESeq2; Fig. 5g). Altogether, SNCA expression patterns could be replicated in brain regions of age-matched controls, however changes were larger between brain regions in PD and iLBD cases. We further assessed SNCA expression using PSEA in the AHBA (Fig. 5h) and found that changes were independent of neuronal or other cell-type densities when comparing different brain regions. In the PD datasets, PSEA results were scattered and did not align between the microarray and RNAseq dataset, which might be caused by the small sample sizes and the comparison of different brain regions (Supplementary Fig. 13).
