Fig. 3. Identification of 86 candidate HIV host factors in primary CD4+ T cells.

A Heatmap of the donor-average log₂-normalized HIV-infection rate at each timepoint for each gRNA called as a hit (purple = decreased infection, pink = increased infection). Each gRNA is grouped by the HIV protein the target gene was found to interact with physically and by early- versus late-presenting phenotypes on the far left. Only donors that reached significance were included in the averages; the percent of donors showing the phenotype are indicated in an adjacent, red-colored heatmap. B Box-and-whisker plot of the distribution of log₂-normalized cell counts per day for called dependency factors, restriction factors, and genes with no phenotype; center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers. C Horizontal stacked bar chart representing the percent of factors previously reported to be HIV host factors in the NCBI GeneRIF database (green) per phenotypic designation, Chi-square test and p-value reported below. D Theoretical example of a host–pathogen arms race driving positive selection (top) with a table summarizing genes found under evolutionary positive selection in this study (bottom). The table summarizes the gene under selection (blue = candidate dependency factor, red = candidate restriction factor), the phenotype reported here, the ratio of nonsynonymous to synonymous changes in the gene body (dN/dS), p-value, number of sites under selective pressure, and if selection had been previously reported. A likelihood-ratio test was used to obtain a p-value, by comparing twice the difference in log-likelihoods with the chi-squared distribution with one degree of freedom; the Benjamini–Hochberg procedure was used to control the false-discovery rate.