Physiologic recovery of Mycobacterium tuberculosis from drug injury: A molecular study of post antibiotic effect in vitro and in vivo
Fig 6
Transcriptional recovery in murine samples.
(a) The heatmap shows the batch-adjusted, VST-normalized, scaled gene expression averaged across samples for specified groups of gene categories related to metabolism. (b-d) Average of batch adjusted, VST-normalized, scaled gene expression in each treatment group over time for genes involved in (b) cytochrome bcc/aa3 supercomplex, (c) cytochrome bd oxidase, and (d) protein translation and modification. Each point represents an individual sample, and the lines connect the mean for each time point. Values are centered around the average value for the pre-treated samples so that points above and below zero represent upregulation and downregulation relative to pre-treated, respectively. (e) Heatmap as in (a) for gene categories relevant to cell wall synthesis and maintenance. (f-g) Average expression plots as in (b) for (f) chaperone heat shock proteins and (g) the DosR regulon. (h) Heatmap as in (a) for sigma factors A-M. (i) Hierarchical clustering of toxin genes (N = 73 genes) identified three broad patterns. Dot plots show the average expression for each cluster across time points. Each point represents an individual sample from 2-week treatment (blue) or 4-week treatment (pink). Horizontal lines indicate average values. Values are centered around the average value for the pre-treated samples so that points above and below zero represent upregulation and downregulation relative to pre-treatment, respectively. (j-l) Average expression plots as in (b) for (j) ESX1, (k) ESX3, (l) ESX4, (m) DNA gyrases, (n) the clpP1P2 complex, and (o) oxidative stress.