Figure 3.

Impact of enriched KEGG pathways involved in “cancer specific types”, “immune system”, “signal transduction”, and “infectious disease viral” in HIV-1-infected individuals subjected to ART. (a) Venn diagram representing the overlap of the genes present in enriched KEGG pathways involved in the four KEGG BRITE classifications. (b–e) Cluster heatmap representing the presence of the genes in enriched KEGG pathways related to “cancer specific types” (b), “immune system” (c), “infectious disease viral” (d), and “signal transduction” (e) in HIV-1-infected individuals before ART (ut) and after a short (st) or a long period (lt) of ART, and in elite controllers. (f) Numbers of immunologic signatures enriched by either a complete list of input genes (all genes) or a gene list with the removal of the genes in the four KEGG BRITE classifications in HIV-1-infected individuals after a short (st) or a long period (lt) of ART. (g) Violin plots representing the distribution of adjusted p-values corresponding to immunologic signatures enriched by either a complete list of the genes (all genes) or a gene list with the removal of the genes in the four KEGG BRITE classifications. Statistical significance was calculated using the Wilcoxon test in R with default options. (h) Cluster heatmap representing the abundance of proinflammatory soluble factor signatures enriched by either a complete list of the genes (all genes, column 1 and column 6) or a gene list with the removal of the genes in the four KEGG BRITE classifications in HIV-1-infected individuals after a short (st, columns 7–10) or a long period (lt, columns 2–5) of ART. (i,j) Correlation plots representing the Pearson correlation calculated based on the abundance of proinflammatory soluble factors in HIV-1-infected individuals after a short (i) or a long period (j) of ART. NS > 0.05, ** p ≤ 0.01, **** p ≤ 0.0001. ART; antiretroviral therapy. EC; elite controllers. HIV IS; HIV integration sites.