Figure 5.

Transcriptomic analysis uncovers dose- and time-dependent effects of Bacillus Calmette-Guérin challenge. A, Overlap in DE genes between challenge groups. The first panel shows overlap among a union of DE genes across all challenge groups and posttreatment days. The second panel shows overlap in the DE genes at peak response days for each challenge group. The final 2 panels show the overlap in DE genes on days 15 and 29 among the challenge groups. The numbers in white (top) and black (bottom) indicate the number of up- and downregulated genes, respectively. B, Time trend summarizing the mean log₂ fold change by challenge group relative to prechallenge for DE genes identified at any time point. Error bars indicate 95% CIs of the mean based on 1000 bootstrap replicates. C, Fold change by statistical significance when days 15 and 29 are compared with prechallenge. The y-axis represents the log₁₀-adjusted P value and the x-axis the log₂ fold change for the challenge effect. The black (2 × 10⁶), red (4 × 10⁶), and blue (8 × 10⁶) dots represent DE genes. Orange lines indicate the fold change cutoff of 1.5-fold up/down. D, Log₂ fold change from pretreatment among DE genes identified across posttreatment days for each dosage group. Rows represent DE genes. Columns represent mean log₂ fold change at a posttreatment day. Red, upregulated vs pretreatment; blue, downregulated vs pretreatment. Dendrograms were obtained with complete linkage clustering of uncentered pairwise Pearson correlation distances between log₂ fold changes. DE, differentially expressed; FDR, false discovery rate.