Fig. 6
Effect of WT and chimeric SIVagm infection on cellular gene expression in AGMs. a, d Enrichment scores of gene sets generated from in vivo SIV infection transcriptional profiling experiments (a) or immune-related genes from the KEGG database d. GSEA analysis was used to contrast transcriptome-wide gene expression profiles from day 170 between the WT SIVagm infected samples and each of the chimeric infections. Gene sets with an FDR of <0.25 were considered significant and are indicated by an asterisk. b, c Enrichment plot (upper) and leading-edge heat map (lower) of GSEA analysis of WT vs. GU1N, WT vs. GU, and WT vs. 1N datasets for enrichment of the “SIV chronic immune activation” (b) and “inflammation and immune activation” (c) gene sets. The plot in the upper panels depicts the running enrichment score indicated by the line adjoining data points. Each data point represents an individual gene in the gene set. Genes contributing the most to the enrichment score (Core genes or leading edge genes) are indicated by bolded symbols. Each bar in the stick plot at bottom indicates the position of an individual gene from the gene set within the entire dataset (indicated on X axis). The lower panel depicts a heat map of “leading edge” or “Core” genes from the enrichment plots. The genes in the leading edge of all three GSEA contrasts (WT vs. GU1N, WT vs. GU, and WT vs. 1N) were pooled, and normalized to the mean of the WT genes. Genes are ranked according to their position in the WT vs. GU1N analysis. Color scale shown at bottom
