Fig. 4

Comparison of the RNA-seq dataset to previously published data and SynGO enrichment analyses. a Upper panels: there was a substantial overlap in subthalamic nucleus (STN) and globus pallidus interna (GPi)-specific terms between our transcriptomics datasets and the anatomically specific expression datasets in Allen Brain Atlas [29]. Our STN data also had 86% overlap with the BTI dataset. Bottom panel: 90% of transcripts common to all samples in our RNA-seq dataset were also found to be common with Human Protein Atlas (HPA) basal ganglia-specific expression dataset [31]. b The gene expression patterns of 13 proteins, that were identified by Biswas et al. [32] to be differentially expressed in the basal ganglia between the left and right hemispheres, also clustered according to hemisphere in the clustering analysis based on our RNA-seq data. We tested the top 20% expressed RNA-seq identifiers common to all analyzed samples (n = 1980) using the SynGO Knowledge base gene set enrichment tool [33]. c Ten terms in the cellular component category and d 11 terms in the biological process category were significantly enriched at 1% FDR (testing terms with at least three matching input genes)