We identified 239 isoforms differentially expressed between SCZ cases and controls: 94 up-regulated and 145 down-regulated. These isoforms derive from 223 genes, which are enriched, as expected, for overlap with the 693 differentially expressed genes (P = 2 × 10−131, Fisher’s exact test), and 136 are differentially expressed at both the gene and isoform levels (Supplementary Fig. 11). No obvious unifying biological theme emerges from this set of genes and isoforms on the basis of pathway enrichment analysis (Supplementary data file 4). An assessment of the impact of age at death or cell type proportions suggests that these variables do not explain significant differential expression (Supplementary Fig. 12). Although analyses of experiments performed using either monkeys or rodents indicate that genes whose expression are affected by antipsychotics are often the same as those we find altered in individuals with SCZ, the impact of antipsychotic drugs nevertheless tends to be significantly in the opposite direction of that observed in the SCZ subjects (Supplementary Table 2). Thus, our analyses find that genes highlighted by the contrast of SCZ cases versus control subjects
