For the WGCNA, only by using a very liberal p value of .10 as the cutoff for gene inclusion (2137 genes) did the resultant network meet the criteria for scale free topology (Zhang and Horvath, 2005). With β = 12, the soft-threshold R2 value was 0.85 with a slope of −1.79. Median connectivity was 3.18 and maximum connectivity was 38.63. Not including the grey module of uncorrelated genes, there were 4 modules with 100 genes or more (Yellow, Blue, Turquoise, and Brown). The Yellow module is a neuron-enriched module and contained 350 genes. The Blue module is an astrocyte- and oligodendrocyte-enriched module and contained 597 genes. The Yellow module had several GO categories (Table 5) that did not appear in the other GO analysis, e.g., G-protein coupled receptor signaling, transmission of nerve impulses, and regulation of membrane potential. The Blue module had some significant categories that were consistent with the results of the GO, KEGG, and Ingenuity analyses of significant (FDR = 0.10) genes (Tables 2–4), e.g., steroid biosynthetic process, sterol metabolic process. In addition, the Blue module had significant GO categories associated with lipid, fatty acid, and phospholipid metabolism (Table 5).
