Modeling Fkh2p-Mcm1p cooperativity improves the ability to identify cell-cycle genes. Scores for the area under the receiver operating characteristic curve (ROC AUC) are plotted as a function of the maximum distance over which cooperative interactions between Fkh2p and Mcm1p are allowed to occur. Different symbols correspond to different assumed values for Kdimer, a parameter that specifies the strength of cooperative interactions (10-1 (circles), 10-2 (squares), 10-3 (diamonds) and 10-4 (triangles)). The horizontal gray line indicates the ROC AUC value in the absence of cooperative interactions with Mcm1p. All calculations were performed using the optimal regulatory region definition previously determined for non-cooperative binding (Gaussian weight function with mean = 250 base pairs (bp) and SD = 250 bp).