The impact of regulation on plant energy metabolism.

<p>The impact of regulation on plant energy metabolism.</p

Example patterns with a) two or b) three stability conditions each.

<p>For each enzyme-metabolite pair, a threshold for the saturation is given. Enzymes are marked in red, their reactants are marked in green. Pattern 1 exhibited an average Laplace ratio of (, ). Pattern 2 affected less training samples because of its less strict threshold on the parameter associated with PGK and GAPDH but also produced more training errors and a lower Laplace value ( , ). Pattern 3 affected an even larger number of hits but nevertheless, it produced fewer training errors than pattern 2. As a consequence, it exhibited the highest Laplace value of all the depicted patterns (, , ).</p

Network underlying the SK-model of the CBC and related pathways.

<p>Compounds written in italics represent external substances the concentrations of which are kept constant in the model. Dotted lines indicate the reactions of cofactors. Dashed lines connect metabolites that are assumed to be in equilibrium so that their concentration changes are directly proportional to each other. The proportions of the individual concentrations of these metabolites then depend solely on their equilibrium constants.</p

Isolated CBC subnetwork.

<p>Isolated subnetwork after restriction to metabolites which are exclusively used by the CBC. Compounds written in italics represent external substances the concentrations of which are kept constant in the model. Dotted lines indicate the reactions of cofactors. Metabolites connected by dashed lines are assumed to be in equilibrium.</p

Stable steady states for increasing values of regulatory TPT parameters.

<p>Effect of increasing SK-model parameters for the triose-phosphate translocator (TPT) under different assumptions regarding regulatory mechanisms. Transporter-associated model parameters were sampled from consecutive intervals of length 0.1. For each interval, SK-models were generated.</p

The principles of structural kinetic modeling.

<p>Normalization of the pathway-specific stoichiometric matrix with respect to steady state concentrations and fluxes produces the normalized matrix . Together with the model parameters in the matrix , it uniquely defines the Jacobian matrix of the system in the steady state. Evaluation of the eigenvalues of the Jacobian matrix then indicates whether the steady state is stable.</p

CBC enzyme occurrences in the derived patterns.

<p>CBC enzyme occurrences in the derived patterns.</p

Classifier performance.

<p>Classifier performance.</p

Enzyme occurrences in the derived patterns (ATP, starch and sucrose metabolism).

<p>Enzyme occurrences in the derived patterns (ATP, starch and sucrose metabolism).</p