In order to identify transcriptionally regulated reactions, a correlation between expression and flux changes was searched for. For this, the method of random sampling (22) was applied to generate 3,292 possible flux distributions for each of the conditions and constraints considered according to the measured external fluxes. Loops were avoided by setting the default bounds for the metabolic fluxes to infinity and negative infinity instead of 1,000 and −1,000, as is usually done. In order to obtain significance scores for the flux change in each reaction, the first sample of condition A (exponential phase) was compared with all the samples of condition B (stationary phase). The number of times that condition A had a higher or lower value for each reaction was subsequently computed. Then, the same procedure was repeated for the second sample of condition A, and this procedure was continued until the last sample of condition A was analyzed. The probability score for a flux increase or decrease is reflected by the fraction of 3,292 × 3,292 comparisons in which condition A had a higher or lower value than condition B. This probability score was subsequently compared with the probability scores of transcriptional changes. A correlation of the significance scores of both flux and transcript hints toward a transcriptional regulation of this reaction.