CD4 and HIV-1 infection: To address the effect of HIV-1 infection on gene expression, we used the four transcriptome datasets obtained from different conditions: CD4+ T cells isolated from infected individuals (Sedaghat et al., 2008) and infected humanized mice (Yamada et al., 2018), and MT-4 cells and the primary CD4+ T cells and infected with HIV-1 in in vitro cultures (Lichinchi et al., 2016) (Table 2).