Supporting Information - Dresch et al. 2010
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چکیده
The root mean square error (RMSE), as implemented in the Fakhouri et al. study, was calculated using Giant protein concentrations as model inputs and the corresponding lacZ mRNA concentrations as outputs [1]. Data points were taken at 20 different Giant concentration levels, uniformly ranging from 0 to 1. Each term in the RMSE was weighted by the number of actual data points over which each lacZ concentration was averaged. In our sensitivity analysis, this weighted RMSE was used as the objective function. The Pearson correlation coefficient, as implemented in the Zinzen et al. study, was calculated using Dorsal, Twist, and Snail protein concentrations as model inputs and the corresponding rho and vnd mRNA concentrations as outputs, which can be found at DVEx database (http://www.dvex.org) [2]. Enhancer-like structures used to calculate sensitivities of the Zinzen et al. model For the results shown in Figure 3, we used two representative pairs of enhancer structures proposed by Zinzen et al.. The remaining structures were analyzed as shown in Figure S7. Each representative pair of enhancer structures is defined by the number of modules and binding sites in each of the representative enhancers. An enhancer with more than one module (Md > 1) is assumed to have identical, independent modules contributing to the expression of that gene. D, T/S, T, and S represent the number of binding sites for Dorsal, Twist/Snail, Twist, and Snail, respectively, in each module. A T/S binding site differs from other binding sites in that it can be occupied by either the Twist or Snail protein. The first set of representative enhancers has, for the rho-like
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