Fig. 3

WGCNA network. (a) The WGCNA network has 19 modules, which we labeled using gene ontology enrichment analysis. To simplify the representation further, we hierarchically clustered the eigengenes to identify 5 superclusters, and color-coded them with distinct colors. Here, the turquoise supercluster can be understood as the adaptive immune system, the brown supercluster as components of the innate immune system, blue as a metabolic module, green as a catabolic module, and yellow as a reparative supercluster. The 4 most populated modules are T cells, catabolism, innate immunity, and mitochondria, all from separate superclusters. (b) WGCNA computes the eigengene network links using Pearson correlation, which we threshold at r > 0.3 for display. The color of each link indicates positive (red) or negative (green) correlation. The width of each link is proportional to the magnitude of correlation. The size of each node is proportional to the eigenvector centrality in the network. Notice the strong negative correlations between the innate and adaptive immune superclusters, the positive correlations of the mitochondria module with the innate module, and the negative correlations of the mitochondria module with the adaptive immune supercluster. The demethylation module is relatively disconnected, and is comprised mostly of Y-chromosome genes