Figure 5. Identification of differentially expressed genes in vRNA⁺ cells.

(A) Schematic overview showing experimental design. (B) Volcano plot of differentially expressed (log₂ fold change > 0.3, P_adj < 0.05, Wilcoxon’s rank-sum test) genes in HIV vRNA⁺ cells compared with vRNA^– CD4⁺ T cells across all samples (blood and colon, stimulated and unstimulated cells). Upregulated genes in red, downregulated genes in blue. (C–F) Volcano plots of differentially expressed genes, as in B, specifically within the indicated sample conditions. (G) Differentially expressed surface proteins between vRNA⁺ cells and vRNA^– cells before correction for multiple testing. (H) As in G, but after Bonferroni’s P value correction for multiple testing.