Fig. 3

Replication co-expression analysis of microglial transcriptomic datasets across neuroinflammatory and neurodegenerative disease models. a Cluster dendrogram summarizing results of validation WGCNA performed using 64 existing Nanostring purified microglial transcriptomic datasets (369 genes in common across all conditions). Datasets included aging WT and APP/PS1 models (age range 2–17 mo, n = 24), WT and SOD1-G93A transgenic mice (n = 13), control and various stages of EAE in mice (n = 21) and WT and intra-cerebral LPS-treated WT mice (n = 6). Expression data were first batch-corrected followed by WGCNA to identify modules of highly co-expressed genes. b Module over-representation analysis (ORA) of derivation (43 microglial arrays, y-axis) and validation WGCNA (64 microglial Nanostring transcriptomic datasets, x-axis) studies. Module overlap was assessed by Fisher-exact test and the negative log₁₀ transformed false discovery rate (FDR) for overlap is indicated by color intensity. Validation modules are numbered (M1–19) while derivation modules are indicated by the original color scheme. c Module eigengene expression and trajectories of change in module expression across various traits in the Nanostring co-expression dataset. Validation modules highlighted here were chosen based on strength of overlap from the over-representation analysis. M6 and M7 are representative of the Blue homeostatic derivation module. M4 is representative of the Yellow anti-inflammatory derivation module while M3 is representative of the Magenta pro-inflammatory derivation module. M1 is representative of LPS-induced Midnightblue derivation module while M19 is representative of the IL4-upregulated Cyan derivation module