Fig. 2
From: Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration
RIGs are proximal to super-enhancers regardless of their expression. a Regularized log-transformed read counts on protein-coding genes averaged over three replicates in activated CD4+ T cells shown as violin plot for genes without HIV-1 integrations and genes with HIV-1 integrations. b Box plot for protein-coding genes grouped by number of HIV-1 lists they appear in. c Box plot for protein-coding genes grouped by the number of HIV-1 lists they appear in, with RIGs grouped together in ≥2 lists’ group. Box plots are shown separately for genes that have super-enhancer 5 kb upstream of TSS or super-enhancer overlaps them (SE in proximity) and genes that do not have super-enhancer in proximity. Differences in median abundances of mRNA are statistically significant for all groups (p value <2.2 x 10−16 for genes without HIV integrations and genes found on only one list and p value 3.7 × 10−12 for RIGs, calculated by Wilcoxon rank-sum test). d Bar plots show the percentage of protein-coding genes that have super-enhancer in proximity, arranged by number of lists the gene is found in and by expression group
