None of the DE genes at FDR < 0.05 overlapped between multiple brain regions. Therefore, the less conservative significance threshold of FDR < 0.25, which was also used for downstream analyses, was applied to compare the overlap of DE genes. At FDR < 0.25 the cardiomyopathy associated 5 (CMYA5) gene showed an upregulation in both caudate nucleus and putamen. ARHGEF15 (Rho Guanine Nucleotide Exchange Factor 15) was upregulated in all three brain regions at FDR < 0.25. The Top 5 DE genes from each brain region are listed in Table 2; complete summary statistics are listed in Supplementary Table S2 (CN), S3 (PUT), and S4 (VS). Overlap between DE genes in the different brain regions is shown in Fig. 2A.Table 2Top 5 differentially expressed genes in caudate nucleus, putamen, and ventral striatum.Entrez Gene IDGene namebaseMeanlog2(FC)lfcSEStatP-ValueFDRCaudate nucleus9654TTLL41125.890.110.025.592.33 × 10−80.00052624GATA251.17−0.270.05−4.928.58 × 10−70.009125904CNOT10695.680.060.014.841.27 × 10−60.0091222256CDHR31483.680.190.044.751.99 × 10−60.0106375611SLC26A563.800.280.064.623.81 × 10−60.0163Putamen1674DES22.06−0.860.18−4.702.64 × 10−60.04862050EPHB4118.04−0.190.05−4.192.78 × 10−50.09399144SYNGR2499.84−0.200.05−4.192.76 × 10−50.093955741EDEM2348.56−0.070.02−4.232.30 × 10−50.093984245MRI1662.19−0.130.03−4.133.57 × 10−50.0939Ventral striatum81570CLPB1188.85−0.110.02−4.565.16 × 10−60.065322899ARHGEF1554.23−0.260.06−4.497.04 × 10−60.065355584CHRNA95.58−1.170.26−4.449.14 × 10−60.0653100463488MTRNR2L104.91−2.070.50−4.163.23 × 10−50.1730389161ANKUB130.261.350.344.025.79 × 10−50.2480
