Fig. 2

The M.tb mRNA signatures 7 and 14 days into chemotherapy resemble untreated bacilli. a Hierarchical clustering of M.tb transcriptional profiles derived from sputa before the start of drug therapy (D0, black) and 3, 7 and 14 days into chemotherapy (D3, red; D7, blue; D14, purple). The dendrogram is derived from clustering all genes (4456) and all sputum samples (52) after median centring. Individual patient study numbers are marked. b M.tb genes significantly differentially expressed over time in sputa; at day 3 (top panel), day 7 (middle panel) and day 14 (bottom panel) compared to pre-chemotherapy (day 0) bacilli. Log2 expression ratios are plotted 3, 7 and 14 days after the start of drug therapy; the y-axis detailing fold change relative to day 0. Red colouring marks up-regulation, blue repression. c Table detailing M.tb responses to the early stages of drug therapy. The number of genes significantly induced (red) or repressed (blue) in pairwise comparisons of sputum time points are marked in the matrix. The mean Spearman’s rank correlation scores between samples at each time interval are also detailed (across the diagonal), demonstrating that variation in replicate sputa at each time point did not bias the statistical testing