A UPUC cluster may then be defined as a reaction subset that connects a set of UPUC metabolites. Besides the high essentiality of these UPUC reactions, which is one of the key issues in [19], they comprise also some other quite interesting features, e.g., proportionally fixed steady-state fluxes and significant correspondence with gene-regulatory modules [19]. We would like to point out that the UPUC category, as defined above, has not been used Inhibitors,research,lifescience,medical in the original study of Samal et al. [19], but rather a set consisting of reactions that are either associated

with UP or UC metabolites. Synthetic accessibility (SA), defined by Wunderlich and Mirny [20], is influenced by a measure used in chemical drug design describing the number of steps needed to synthesize a specific compound from a given set Inhibitors,research,lifescience,medical of compounds. Accordingly, the SA for a metabolic system is defined as the minimal number of reactions needed to reach a set of BMS-907351 price outputs (e.g., biomass) from a given set of inputs (e.g., medium composition) as obtained by a breadth-first-search traversal that can only proceed if all needed substrates are available. SA is Inhibitors,research,lifescience,medical successful in predicting essential genes, as many lethal mutations lead to an increase of the SA [20]. For this work we choose to treat SA as a reaction category

by assigning an SA label to every reaction whose knock-out causes a change in biomass SA. Figure 1a shows a schematic representation of metabolism with three exchange reactions (X1, X2 and X3) with the

environment and a two-component biomass reaction (BM). Circles represent metabolites, while boxes stand Inhibitors,research,lifescience,medical for Inhibitors,research,lifescience,medical reactions in this bipartite graph view of a metabolic system. In this Figure, R1 (highlighted in blue) is an example of an SA reaction, as it represents one of the shortest paths to BM, while R5 (highlighted in green) is consuming and producing only metabolites, which are uniquely produced (UP) and uniquely consumed (UC), and thus is an example of a UPUC reaction. Figure 1b–e provides a qualitative impression of the wild-type flux distribution (Figure 1b) and the re-routing of fluxes upon R1 and R5 knockout (Figure 1c,e), respectively. Figure 1 Network context of topological reaction categories. (a) of Simple scheme of a small fictitious metabolic reaction system with examples of UPUC and SA reactions. (b) Wild-type network. (c) Knockout of SA reaction R1. Fluxes are rerouted over R4 leading to … In the example in Figure 1, both reactions (R1 and R5) have an alternative path that goes along reaction R4. Thus, both reaction labels would in this case not serve as a reliable predictor of the reaction’s essentiality.