Comparison of pure-microglia and brain tissue-derived microglia-enriched modules. a) Consensus co-expression networks of brain tissue transcriptomes. Co-expression networks were generated for the indicated brain tissue transcriptome datasets. b) brain tissue consensus module expression boxplots. The ME of the green microglia-enriched module in the Me7, App-Ps1, Aging, and rTg4510 datasets was significantly up-regulated in all model systems. ME expression across all datasets and conditions is depicted as box-and-whisker plots. c) Scatterplot of the hub genes of the consensus pure microglia module and the brain tissue microglia-enriched module. For each gene, which was significantly associated to the pure microglia or the brain tissue microglia-enriched networks, module membership values for the brain tissue green and microglia modules were plotted. Top-50 most connected hubs genes from brain tissue to pure microglia were assigned one of five colors (filled dots). “Pure microglia” (blue), “Mainly pure microglia“ (dark-blue), “General microglia” (black), “Mainly brain tissue-derived microglia signature” (dark-green) and “brain tissue-derived microglia signature” (green). d) Heatmaps of pure microglia to brain tissue microglia-enriched categories. Heatmaps of the consensus profiles of pure microglia and brain tissue datasets as indicated are depicted. Hub genes were assigned by module membership, the top-35 most correlated genes from the pure microglia and brain tissue microglia-enriched consensus modules were categorized in 5 categories as described in c).