Figure 1

Evolutionary pattern of the protein coding genome in primates. Probability density curves of continuous dN/dS values for genes (A) upregulated in CD4+ T cells and in lymph nodes during infection with HIV-1 in vivo in humans, (B) genes differentially regulated during infection of humans with other pathogens and (C) datasets of human innate immunity genes including: an innate immune specific set (Innate DB), genes curated by the Immunogenetic Related Information Source (IRIS) and a manually curated list of immune genes (Immunome), the NCBI HIV interaction database (Interaction DB), the global landscape of HIV-human protein complexes from Jaeger et al. (Jaeger) [15], and of genes associated with Mendelian disorders in OMIM. The kernel smoothed density estimates (density) of dN/dS values for sets of genes is plotted. The height of the curves is relative to the number of genes with the observed dN/dS values. The genome-wide background dN/dS values for 17,755 genes is shown in grey. Statistically significant differences (Kolmogorov-Smirnov statistics p ≤ 0.05) were observed for distributions towards greater dN/dS values for genes differentially expressed in CD4+ T cells and lymph nodes during HIV-1 infection, in infection with Dengue virus, Salmonella typhic and tuberculosis, and for distributions towards smaller dN/dS values for genes involved in HIV-1-human interaction datasets and in the catalog of Mendelian disorders.