The above analysis was focused on the characterization of individual genes whose expression was affected by 22q11.2 deletion. It is equally, if not more important, to uncover gene networks that may be disrupted in the SZ neurons, as many genes function together whereas they may not all show significant expression change. We thus performed WGCNA analysis and detected 15 modules, 13 of which showed no significant differences in module structure between the two conditions (i.e, preserved modules) (Fig. 3a). The two modules below preservation thresholds (light-cyan and green-yellow) had very small numbers of genes. The light-cyan module contained 38 genes in total, 36 of which were from 22q11.2 deleted region; thus its lack of preservation is expected. The green-yellow module was comprised of 92 genes, most of which had an extreme outlier of expression values from one particular control sample (Ctrl_iPS2C). The outlier was the cause of low preservation score. Therefore, the WGCNA results suggest that there is no global gene regulation re-wiring in the SZ neurons. This is in accordance with three previous gene network studies carried out on patients with psychosis [81, 82], which also did not observe a significant perturbation of gene modules in patient samples.
