from untreated, incubated samples from a subset of 59 individuals were used to regress out expression changes attributable to incubation from the treated samples. Data across all four conditions were available from 228 individuals, permitting cross-treatment comparison. As anticipated, treatment induced significant changes in monocyte expression profiles (table S1) with hierarchical cluster analysis demonstrating that group membership was defined by treatment (fig. S1). Analysis of differential gene expression was consistent with biological expectations in terms of identified canonical pathways, the most significant upstream regulators, and the transcriptomic differences between early and late responses to LPS (table S1 and fig. S1) (17).
