We constructed Bayesian networks for each co-expression module. While many of the LOAD-associated network modules are of potential interest, the reconstruction of the Bayesian network for the immune/microglia module is highlighted given it has the strongest disease association based on clinical covariates and network-associated properties: (1) significant differential connectivity of the cortex specific immune modules in LOAD (MDC between 49 and 100% GOC at FDR < 0.001); (2) the immune/microglia module showed the most significant enrichment of functional categories; (3) the highest degree of gene expression correlation to several measures of LOAD neuropathology; (4) the PFC version of the module was highly enriched for brain eSNPs. To increase the predictive power of inflammation related regulatory networks, we further built up the directed Bayesian network for the inflammation modules derived from the individual brain regions. Figure 5 highlights the interactions within and between the five predominant immunologic families in the PFC-based putative microglia module. To generate this roadmap to the complex structure of the immune/microglia module, genes which were not direct members of one of these five core pathways were assigned
