The abstract representation in our model of the network shown in Figure 1(a) is shown in Figure 1(b).

<p>The gene corresponding to each protein is represented by different colors. Each protein (colored gray) has a certain number of binding domains. For eg., protein P1 can bind to genes G1, G3 and G4 (showed by the colored bars). The red and green boxes refer to the effect of binding while the red and green circles refer to PTMs.: red represents repression and green, activation</p

Factor Loadings–Correlation coefficients between original variables and components

<p>Factor Loadings–Correlation coefficients between original variables and components</p

The original (template) network that gave rise to the data and the two best networks obtained from minimizing the error.

<p>Only the network connections were optimized in this case, with the kinetic parameters taking on the same values as those that generated the “data”. Both Optimized Network-1 (Figure 3(b)) and Optimized Network-2 (Figure 3(c)) had a value of 0 for the minimization function which was the RMSD of the model and the “data” values.</p

The original (template) network that gave rise to the data and the two best networks obtained from minimizing the error.

<p>The network connectivities as well as the reaction probabilities were optimized in order to obtain the minimal deviation between the model and “data” values.</p

The optimal (template) network and the best network inferred from minimizing the RMSD between the two expression levels.

<p>Only the network connectivities were optimized. All other parameters including the kinetic parameters were kept constant. Although the two networks are very similar, there is a slight difference in the activation of P1 and P2.</p

Factor scores for the first four principal components.

<p>The different colored lines are the natural separation of the results into the different simulation runs.</p

Correlation coefficient of the individual runs for the three different networks against one another.

<p>The correlation coefficients are computed as the correlation of the three protein levels for each run and plotted as a matrix with the different runs making up the abscissa and ordinate. Runs 1–25 pertain to the template network, 26–50 to the first optimized network (R2) and runs 51–75 to the second optimized network (R3). The colors range from blue (very low correlation) to dark brown (high correlation). The fact that there is no clear discrimination between the networks implies that the protein levels obtained from the three networks occupy similar regions in phase-space.</p

Protein Levels for both experiments: (5(a)): The case where only the network connections are optimized.

<p>(5(b)): Case were network connections and reaction probabilities are optimized. Notice that in both cases, the protein expression patterns are very similar despite the differences in network connectivities as seen from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000562#pone-0000562-g003" target="_blank">Figures 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000562#pone-0000562-g004" target="_blank">4</a>.</p

Eigenvalues and the percent of explained variance

<p>Eigenvalues and the percent of explained variance</p

The template network (a) and the protein levels (b) that mimic “experimental data” values.

<p>The template network (a) and the protein levels (b) that mimic “experimental data” values.</p