General description of thermodynamic models and examples of constructs, data sets, and formulas used for the models of Zinzen et al. and Fakhouri et al. A) Thermodynamic models. The first column shows the probability of a transcription factor binding. Square brackets denote protein concentrations and K values represent binding parameters. The second column illustrates all possible states of an enhancer containing one repressor and one activator binding site, the third the probability of each occurring and the fourth the expression contribution for each. The last column shows how the total expression is calculated, as a sum of each states' probability multiplied by its expression contribution. B) Examples of the implementation of the Fakhouri et al. model. The first column gives examples of two constructs used, the second representative embryos from each, imaged for lacZ reporter gene activity, the third the actual normalized repressor [Gt] versus reporter gene [lacZ] levels used for modeling, and the last the model's total expression formulas. For sensitivity analysis, the RMSE is calculated using the model formula for each of the twelve constructs; this figure shows only two examples (other constructs described in ). C) Examples of the implementation of the Zinzen et al. model. The first column lists two conceptual constructs used. These are not depicted as in A) and B) because the Zinzen et al. model does not consider order or spacing of binding sites. Enhancers are described solely by the number of binding sites. Terms inside brackets indicate the presence of binding sites for that protein, while subscripts indicate the number of binding sites. The second column contains quantitative data of normalized [Dl], [Twi], and [Sna] proteins and [rho] mRNA used for modeling the rho enhancer. The last column gives the model's total expression formulas for each of these conceptual constructs.