Figure 5: Frequency of HIV-1 integration events in genes linked to clonal expansion of latently HIV-1-infected CD4⁺ T cells.

(a) Each HIV-1 integration site data set was first divided into two groups: one comprises genes in which two or more HIV-1 integration events were identified (gene hotspots) and the other comprises genes in which only single HIV-1 integration events were identified. The frequency of genes linked to clonal expansion of latently HIV-1-infected CD4⁺ T cells in the two groups of genes for each data set was determined and the ratio was computed. (b) Ratio of frequency of genes linked to clonal expansion of latently HIV-1-infected CD4⁺ T cells in gene hotspots to in genes with single HIV-1 integration events. Autologous and heterologous HIV-1 data sets were combined here (closed symbols). Details of data sets derived from other studies (open symbols) are found in Table 2. Each random control comprised 5,000 random genes generated in silico instead of genes linked to clonal expansion of latently HIV-1-infected CD4⁺ T cells. Two random controls were analysed for each data set. Two-tailed Mann-Whitney U test with 95% confidence interval was used to test for statistical significance.