Fig. 2
Comparisons of the effect of HIV infection on cellular gene expression to additional studies comparing transcription in subsets of immune cells. The MSigDB database was used to extract 185 sets of differentially expressed genes from pairs of transcriptional profiling studies of immune cell subsets involving CD4+ T cells. For each pair of studies, we used Fisher’s exact test to measure the association between up- and downregulation calls for genes identified as differentially expressed in both our HIV study and the comparator immune subsets. a The transcriptional profiles with strongest associations with changes observed in our study of HIV89.6 infection of primary T cells. Blue indicates a positive association between changes seen in HIV-infected cells and the first immune subset (text colored blue) while red indicates a positive association with the second immune subset (text colored red). The color scale shows the conservative (i.e. closest to 1) boundary of the confidence interval of the odds ratio. For confidence intervals overlapping 1, the value was set to 1. Therefore all colored squares indicate significant associations. b As in a, but showing the transcriptional profiles most strongly associated with changes observed in lymph node biopsies from acutely infected patients [30]