Fig. 1

Validation of prediction of changes in MTB metabolite production during changes in oxygen. a The predicted change in maximum flux through each metabolite with a corresponding metabolomics measurement is plotted against the log2 fold change in concentration from just prior to hypoxia and 1-day post hypoxia. Error bars represent standard deviations of predicted changes calculated across the 1000 samples in the case of model predictions and across 4 replicates in the case of experimental measurements. MFC values for all model metabolites are provided in Additional file 1: Figure S1. b One-thousand samples were generated by randomizing gene labels on the time course expression data. The Spearman correlation coefficient was calculated for each permutation. This distribution is compared with the distribution of coefficients generated from Monte Carlo samples using the correct gene labels. c Spearman correlation coefficient as a function of the parameter κ for predictions of change in metabolite concentration from just prior to hypoxia to 1-day post hypoxia. Error bars represent standard deviations of the Spearman correlation coefficient calculated across 100 samples of the gene expression data. d Changes in the production of several classes of lipids across the full hypoxic and reaeration time course. Red lines show model predictions of normalized net production for each lipid across the experimental time course. Black lines show normalized measured changed in abundance across each time course for each measured member of the lipid class. Error bars represent the standard deviation across samples for predicted production and across experimental replicates for measured abundance values. e Predicted changes in TAG production (red) and consumption (blue) fluxes. Error bars represent the standard deviation across samples for predicted production and consumption