Fig. 3

Gene module discovery reveals shared and distinct temporal features between immune responses to pathogenic and nonpathogenic lentiviral infection. A Overview of gene module discovery by WGCNA, adapted from Kazer et al. [18]. HVG, highly variable gene. B Jaccard index heatmap depicting the degree of overlap in gene membership between all discovered modules. C Expression of modules over time by the cell type and in the animal in which the modules were discovered. For D–G, heatmaps depict average expression of gene modules by the cell type and animal in which the modules were discovered. Scatter plots depict either the module membership of module genes in CL8 and 170 animals (right D, F, and G) or upstream regulators (left E) and transcription factor activities (right E) predicted to result in expression of the observed gene modules. D–E monocyte modules boxed in red in panel (B). F Modules downregulated by monocytes in at least one time point. G DC modules boxed in blue in B