Model residuals. Shown is a comparison of the α-coefficients of transcription factors estimated using regression and displayed in Additional file 3 to those predicted by our dynamical model. We plot the mean absolute value of the α-coefficients across two periods of the cell cycle versus the mean absolute value of the residuals (i.e., the difference between the measured and predicted α-coefficients). Each time step represents a 7-minute interval. We see that the model has significant predictive power, although this diminishes as the cell cycle progresses. This may be due in part to gradual loss of synchrony over time in the experimental yeast cells from which expression was measured.