expressed after correction for multiple testing (FDR ≤ 5%), 332 up-regulated and 361 down-regulated (Fig. 5A, Supplementary data file 3). All had modest fold changes (Fig. 5B), with a mean of 1.09 and range 1.03–1.33 (inverting down-regulated expression ratios). As expected, hierarchical clustering of the differentially expressed genes showed case-control distinctions but were independent of institution, sex, age at death, ethnicity, and RIN (Fig. 5A). We examined differential expression in an independent sample, the NIMH Human Brain Collection Core (HBCC), which generated DLPFC gene expression data using Illumina HumanHT-12_V4 Beadchip microarrays from 131 SCZ cases and 176 controls. Though these arrays differ from RNA-seq in their capture features, there was high correlation of test statistics for differential expression in CMC compared to HBCC for the differentially expressed genes also present in the HBCC data (480 of 693), Pearson correlation r = 0.58 (P < 10−16); the correlation remains high (r = 0.28, P < 10−16) across all 10,928 genes common to both platforms after QC (Fig. 5C).
