(A) Mean Th2, Th1 and Th17 gene module expression over time within Th2, Th1, and Th17 clones (see Methods), respectively, in each treatment group patient at each time point. (B) Fractional expression of Th2, Th1, and Th17 modules within clonotypes of Th subtypes over time. Fractional clonal expression is defined as the proportion of cells within each clonotype expressing their respective module (see Methods). Each data point represents the cells of an individual expanded clonotype from 1 patient at 1 time point. Patients in the placebo group were excluded. (C) Degree of suppression in Th2A-like clones by clinical group. The ratio of mean Th2 module expression in Th2A-like clones from each patient was calculated between buildup and maintenance. Spearman’s rho = 0.74; *P < 0.05. n = 9. Spearman’s test was performed to determine the correlation between ratio and outcome within the treatment group (assigning 2 for tolerance, 1 for partial tolerance, and 0 for treatment failure to represent the ordinal relationship between treatment groups). (D) PC1 score for CD154⁺ cells by outcome. PCA was performed using the 50 gene modules as features and all CD154⁺ cells at baseline as the input data (see Methods). Each data point represents the mean PC1 score for all CD154⁺ cells from a single patient at a single time point. Black-outlined data points represent the baseline time point. (E) Top 5 gene module loadings in PC1. Bar heights represent the magnitude of each contribution to PC1. (See Supplemental Figures 4 and 5 for further details on each gene module.) *P < 0.05 (adjusted), **P < 0.005 (adjusted), and ****P < 0.0005 (adjusted), by paired (A) or unpaired (B and D) Wilcoxon rank-sum test.