Modeling the genome-wide transient response to stimuli in yeast: Adaptation through integral feedback

The gene expression response of yeast to various types of stresses/perturbations shows a common pattern for the vast majority of genes, characterized by a quick transient peak followed by a return to the basal level (adaptation). In order to model this transient and the consequent adaptation, we use the idea of integral feedback (the integral representing the relative concentration of gene products). The resulting linear system with input explain sufficiently well the different time constants observable in the transient response while, at the same time, being in agreement with the known experimental degradation rates measurements.