Differential host gene expression by <i>in vivo</i> SIV-infected T cells.

<p><b>(A)</b> Genes showing a change in expression level or proportion in single cells from one or more infection states compared to uninfected cells in PBMC from one or more animals (n = 4). Significant changes (FDR < 0.1) are indicated (*). Plots display the MAST estimates of average frequency of expression (x-axis) and average expression level in cells when a gene is expressed (y-axis) for each gene by cell infection state (ellipse). Boundaries reflect the 90% bivariate Wald test confidence interval (Chi-square, 2 degrees of freedom). Contours with minimal or no overlap are more likely to be associated with a significant difference. The number of cells analyzed from each infection state is shown in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006445#ppat.1006445.s010" target="_blank">S3 Table</a>. (<b>B</b>) PBMC Z-statistics (standardized model coefficients) show expression across animals and infection stages by combining (using Stouffer’s method) the frequency of expression and continuous expression. Expression is mean centered by row. (<b>C</b>) Venn diagram of DE genes identified by the hurdle likelihood ratio test, common to PBMC from multiple animals. (<b>D</b>) Estimated average expression of four significant genes from (A) by cellular infection state. For each animal, significant differences from uninfected cells (at the 10% level after multiple testing adjustment across 92 genes tested) are marked with an asterisk. Unadjusted 95% confidence bounds are shown for the expression level. (<b>E-G</b>) Analyses of animal AY69 lymph node and jejunum as in (A-C). (<b>H</b>) Venn diagram of DE genes common across tissues within animal AY69. Two genes common to all tissues are indicated. Experiments were performed once for each specimen and all data is shown.