Fig. 4
Repeat categories enriched upon infection with HIV. a The association of repeat regions differentially expressed after HIV89.6 infection of primary T cells observed for varying thresholds of differential expression. The threshold used to call a gene differentially expressed based on the Bayesian posterior median was varied and Fisher’s exact test was used to assess whether any genomic repeats had a significant association with this differential expression. Note that only ERV-9 (annotated as HERV9-int in the RepeatMasker database) and it’s corresponding long terminal repeat ERV-9/LTR12C were significantly associated with large changes in expression. b Enrichment of repeat categories in regions differentially expressed (Bayesian 95 % credible interval \(>2\times\) change) between HIV-infected and control CD4+ T cells. The repeated sequences are ordered on the x-axis by the extent of induction within each class with circles indicating repeats annotated as hominid specific and squares marking all other repeats, the y-axis shows the p value for upregulation after infection. The dashed line indicates a Bonferroni corrected p value of 0.05. c The proportion of human mapped reads that align within classes of genomic repeats for data from primary CD4+ T cells from this study and SupT1 cells from Chang et al. [25]. A single read mapping multiple times to a given category was only counted once