Phenotype of rM compared with pro-inflammatory macrophages. (A) Gene expression of rM is compared with pro-inflammatory macrophages using cells from 6 animals showing a stark contrast in macrophage phenotypes. (B) A sample of the top up- and down-regulated genes in rM cells versus pro-inflammatory macrophages based on FDR of 0.05 and fold expression difference of 1.5. The software package Expander Version 5.1 detected significantly enriched functional gene sets in rM versus pro-inflammatory macrophages, including those for (C) proliferation with key genes enriched for cell cycling shown in panel D and a list of the genes shown in panel E (see Figure 1 continued). The software package Expander Version 5.1 detected significantly enriched functional gene sets in rM versus pro-inflammatory macrophages, including key genes enriched for cell cycling shown in panel D and a list of the genes shown in panel E. In addition to proliferation, other pathways were enriched in rM compared with pro-inflammatory macrophages: (F) immune function. In addition to proliferation, other pathways were enriched in rM compared with pro-inflammatory macrophages: (G) a range of other significantly enriched functional classes.