Fig. 2

Correlation network analysis reveals microglial gene modules. a WGCNA clustering scheme. 1st order clustering was performed on 6215 genes across all core conditions [left]. Each resulting 1st order cluster was then run on WGCNA a second time (2nd order clustering). Example shows 2nd order clustering using the 1st order BR module [center],which yields two 2nd order modules – BR_blue and BR_turquoise. Each 2nd order module comprises a set of co-expressed genes [right]. b Mean intramodule correlation score in 37 modules. Red line represents cutoff threshold for reproducibility. Error bars reresent standard deviation. c Heatmap of mean module eigengene values across 40 core stimulus conditions. Only modules passing quality control criteria are shown. Heatmap scale is in arbitrary units; a red shade indicates that the module is activated in a given stimulus condition, with darker shades corresponding to stronger activation. Blue indicates suppression of a module. Gray mask = n.s. compared to control, *p < 0.05