(A) Ontology profiling of 428 probe sets significantly altered by SIV infection in SMs was based on gene ontology annotations retrieved from the DAVID Bioinformatics Database. Columns represent the number of genes in each ontology cluster listed below the x axis. Enrichment scores were calculated using the human genome as a background. (B) Hierarchical clustering of 428 genes significantly regulated by SIV infection in SMs was performed as described in Figure 1 legend. Clustering was performed on the average of log₁₀ ratios of gene expression relative to levels before infection; fold changes were calculated by subtracting the log₁₀ intensity preinfected measurement from after-infection measurement for individual animals prior to calculating the average. The dendrogram is not shown. (C) PCA of log₁₀ intensity measurements of 428 differentially expressed probe sets. Colored circles represent data set for individual SMs at the time points indicated in the key. Ellipses are centered on the median of the following time points: days 0, 10, and 14. (D) Heat maps of selected innate immunity, adaptive immunity, apoptosis, and cell-cycle regulating genes with differential expression in SIV-infected SMs. Genes were categorized based on annotation in DAVID, Entrez Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene), and Ingenuity Pathway Assist databases and on described function in the literature. Genes covered by multiple probe sets on the array are represented by the highest intensity. Genes were clustered as described in Figure 1 legend. Color scale is shown at bottom and ranges from 2-fold downregulated to 5-fold upregulated.