Similar gene expression profiles between GFP⁺ and GFP⁻ liver macrophages. (A) Heat map displaying expression of the top 1500 expressed genes by RNA-seq. Fragments per kilobase of transcript per million mapped reads expression data are mean-centered and standardized. Hierarchical clustering was performed using 1-minus Pearson correlation, average linkage. (B) Volcano plot showing the number of differentially expressed genes with at least a 1.5-fold change and P < .001 between combined GFP⁺ and GFP⁻ cells compared with control cells. (C) Overrepresentation analysis using the 276 genes with higher relative expression in both GFP⁺ and GFP⁻ cells compared with controls with a P < .1 finds genes enriched in multiple pathways including cell adhesion and granulocyte activation. (D) Gene set enrichment analysis results for genes more highly expressed in controls than GFP^+/− cells. ∗FDR < 0.05. (E) Gene set enrichment analysis results for genes more highly expressed in GFP^+/− compared with controls. FDR, false discovery rate; NES, normalized enrichment score.