Gene expression profiles in monocytes, macrophages, and monocyte-macrophage differentiation. (A,B) Gene expression profiles using cluster analysis of 1,000 genes with highest coefficients of variation arranged by disease status and atherosclerosis phenotype. Panel (A) shows expression patterns in monocytes, and panel (B) shows expression in macrophages. Above each heatmap is a legend: in the upper section, the purple line denotes patients with systemic lupus erythematosus (SLE) and the orange line denotes healthy controls; in the lower section, the blue line denotes individuals with an atherosclerosis phenotype (as defined in the methods section) and the maroon line denotes individuals without the atherosclerosis phenotype. In the monocyte heatmap, note the presence of the interferon signature (denoted by pink bar to right) in nine out of 20 SLE patients and the chemokine signature (brown bar) in three patients, both of which are very enriched compared with controls. (C) Representative heatmap demonstrating downregulated signal transduction genes during monocyte-to-macrophage differentiation after pairwise comparison of monocyte and macrophage expression in all 36 samples. Red (green) pixels indicate more (less) upregulation of expression in macrophages compared with monocytes. (D) Histogram showing fold change (both upregulated and downregulated genes) among genes involved in signal transduction pathway during monocyte-to-macrophage differentiation.