To evaluate gene coexpression across brain regions at different developmental periods for the DEGs from our 22q11.2 del samples, we reanalyzed the RNA-seq gene expression data from the Atlas of the Developing Human Brain (BrainSpan) (http://www.brainspan.org). We performed correlation analysis to uncover genes co-expressed with our DEGs. As described in previous studies [64], tissue samples from the BrainSpan were grouped into four neuroanatomical regions—frontal cortex (FC), temporal and parietal regions (TP), sensory-motor regions (SM), and subcortical regions (SC), and four developmental stages—embryonic stage (8–12 post-conception weeks), fetal (13–26 post-conception weeks), early infancy to late childhood (4 months to 11 years), and adolescence to adulthood (13–23 years) (Table 1). Next, for each of the DEGs, we calculated Pearson correlation coefficients (R) between its expression and that of all other DEGs across tissues within each brain region and at each developmental stage. 46 DEGs were excluded since their expression values were zero in all tissues. Gene pairs with |R| ≥ 0.9 were defined as significantly co-expressed and thus “connected” in subsequent co-expression construction. Network connectedness was measured by the number of connections,
