Additional file 1: of Toll-like receptor 4 in glial inflammatory responses to air pollution in vitro and in vivo

Gene kME relationship between modules: The two shared modules, enriched by both treatments, had strong inverse correlations between the gene-module specific kMEs, which is the eigengene-based connectivity for a gene within a module (nPM, R = −0.994; LPS, R = −0.968). Each gene is given a kME for every module, and then placed into the module of best fit. Thus, individual RNAs with increased expression had strong inverse associations with the eigengene for the turquoise module, while RNAs with decreased expression had strong inverse associations with the eigengene for the blue module. As examples, TNFα had a kME of +0.93 in the blue module, but −0.91 in the turquoise module; again, the subunits NF-κB1 and NF-κB2 had positive kMEs of +0.91 and +0.96, respectively, in the blue module, but negative kMEs of −0.86 and −0.93, respectively, in the turquoise module. Together this suggests that the turquoise and the blue modules represent a single network, where the turquoise comprises the decreased RNAs in the network and the blue comprises the increased RNAs. (ZIP 43372 kb)