Sensitivity of ModuleMiner's performance to the quality of the input genes. The ratio of true positive genes (containing the smooth muscle cis-regulatory module [CRM]) to negative genes (approximated by random genes) was varied. Each time, a leave-one-out cross-validation was performed, a receiver operating characteristic (ROC) curve was constructed, and the area under the ROC curve (AUC) was calculated. These AUCs were plotted as a function of the ratio negative genes/positive genes. Because an AUC of 50% signifies random ordering of the left-out genes (and hence indicates that no CRMs can be detected), this value was taken as the origin on the y-axis. Blue: the number of positive genes was kept constant at ten, and the number of negative genes was varied. Red: the total number of genes was kept constant at ten, and the ratio negative genes/positive genes was varied.