NCan and canonical mice can be distinguished at 5 wk, 2 wk, and baseline. (A) Model classification accuracy for 10 rounds of fivefold cross-validation (CV) compared with a model built on randomly selected features via Mann–Whitney U test (***P < 0.001) at 5 wk. Mean ±1 SD shown as crossbars. (B) Scores plot for LASSO PLS-DA at on lung features at 2 wk after infection (n = 2–4 mice per sex per strain per time point). Each dot represents an individual mouse, and the ellipse marks the 95% group confidence interval. (C) LASSO-selected features for the 2 wk PLS-DA are plotted by their contribution to LV1. (D) Heatmap showing correlation values of features highly correlated (|Spearman R| > 0.7) with LASSO-selected features at 2 wk. (E) LASSO-selected features for baseline spleen PLS-DA model seen in Fig. 4 A are plotted by their contribution to LV1. (F) Average z-scored value of each LASSO-selected spleen feature or highly correlated (|Spearman R| > 0.8, P < 0.01) feature for each mouse strain (canonical = blue, NCan = purple) at baseline. Features are colored by cell type according to inset legend, and measurements were hierarchically clustered. NK, natural killer cell; DC, dendritic cell; Treg, regulatory T cell.