Effect of transcriptional synergy on model performance.

A DirectInt model with or without transcriptional synergy (“Synergy = N(o)” versus “Synergy = Y(es)”) was evaluated by the average correlation coefficient (“Avg. CC”) on the 37 CRMs in the data set, as well as the average CC under 10-fold cross validation (“CVCC”). “Synergy = No” is implemented by setting NMA = 1 for the two activators (Bcd and Cad), while “Synergy = Yes” amounts to setting NMA = ∞. The evaluation is done in the presence of Bcd and Cad self-cooperative binding (“Cooperativity = Y”) as well as in the absence of any DNA-binding cooperativity (“Cooperativity = N”).