We examined whether genes implicated in genetic studies are more likely to affect hub nodes (genes with higher number of connections) in the M2c module. For each gene in the M2c module, we estimated the intramodular connectivity (connectivity of nodes to other nodes within the M2c module). We then examined whether genes that have association for common GWAS variants (PGC SCZ2 GWAS loci), CNVs or de novo mutations have higher intramodular connectivity compared to genes that are not genetically associated with SCZ. We found a significant effect for PGC SCZ2 GWAS loci (T test: t = 2.6; P = 0.013) and de novo mutations (T test: t = 5.1; P = 2.9 × 10−6) but no CNVs (T test: t = 0.88; P = 0.4), where genes associated with SCZ have higher intramodular connectivity. Nodes from the top 50 hub genes that have been associated with SCZ are illustrated in Figure 6C.
