Fig. 3

Features of proteomics and transcriptomics datasets obtained from the RNA sequencing and LC–MS analyses of the patient-derived brain tissues. The sample encoding indicates the patients’ disorders as follows: Parkinson’s disease (PD, n = 13), genetic dystonia (DYT, n = 3) and tremor (TRE, n = 1). a The number of expressed genes in each sample. b Principal component analysis plot of the gene expression data. c Hierarchical clustering, colored based on the hemisphere, shows that the samples tended to cluster according to the DBS target region. d Venn diagrams showing the number of common genes identified in the samples from the subthalamic nucleus (STN) and the globus pallidus interna (GPi). e The number of identified proteins in each sample, colored based on whether blood was visible in the sample. No statistical difference was observed in the number of proteins identified (P = 0.51, t-test). f Principal component analysis plot of the proteomic data. g Hierarchical clustering, colored based on whether blood was visible in the sample, shows that samples with visible blood tended to cluster