Comparison of measurements and model predictions on the leucine biosynthesis model. The expression levels (both predicted and observed) are indicated in yellow to blue scale (low to high expression). Discrepancies are indicated in green (observed < predicted) to red (observed > predicted) scale. (a) The data collected for the leucine biosynthesis model. Rows correspond to mRNA variables and columns correspond to experiments. Cells are colored according to their observed expression levels. Black cells correspond to cases where the mRNA was not measured. The black strip in the top portion of LEU3m cells indicates that it was perturbed in the respective experiments. (b) The discrepancy matrix, highlighting differences between measurements and predictions. Rows correspond to mRNA variables and columns to experiments. Each cell contains two squares colored in expression scale, where the left square indicates observed level and the right indicates the predicted level. The background color intensity indicates the discrepancy between the observed and predicted levels. (c) The observed and predicted expression levels for a nitrogen limitation experiment eight hours after treatment (Gasch et al. , matrices A, B column 20) projected on the model canvas as two colored strips above each variable. The strip right above the variable box represents the predicted level. The strip above it (available only for mRNA variables in this case) represents the observed level.