Gene networks were constructed using the WGCNA as described elsewhere (Colville et al., 2017). Initially all genes meeting the expression criteria of one CPM were entered into the analysis using a consensus module approach (Iancu et al., 2010). The number of genes in each network was then culled to include only those genes that contribute >80% of the total network connectivity. It was these reduced sets of genes (∼6,500/region) that were entered into subsequent analyses. Modules were color coded arbitrarily within or across regions. Supplementary Table S2 also provides annotation for which network modules were significantly enriched in genes associated with neurons, astrocytes, and oligodendrocytes (Cahoy et al., 2008). We investigated the interaction subnetwork of Dlg2, a gene affected by selection and well-connected in the network. Utilizing the GeneMANIA (Warde-Farley et al., 2010) software as implemented in the associated Cytoscape (Shannon et al., 2003) plugin, we found a number of non-transcriptional mechanisms by which Dlg2 interacts with other members of the glutamate family (Figure 1).
