Modular decomposition of metabolic systems via null-space analysis

• Published in: Journal of theoretical biology Vol. 249; no. 4; pp. 691 - 705
• Main Authors: Poolman, Mark G., Sebu, Cristiana, Pidcock, Michael K., Fell, David A.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 21.12.2007
• Subjects: Algorithms; Computer Simulation; Dendrogram; Escherichia coli - metabolism; Flux correlation coefficient; Genome scale; Metabolic model; Metabolic Networks and Pathways - physiology; Models, Biological; Null-space; Photosynthesis; Streptomyces coelicolor - metabolism; Metabolic model; Null-space; Dendrogram; Genome scale; Flux correlation coefficient
• ISSN: 0022-5193; 1095-8541
• DOI: 10.1016/j.jtbi.2007.08.005

We describe a method by which the reactions in a metabolic system may be grouped hierarchically into sets of modules to form a metabolic reaction tree. In contrast to previous approaches, the method described here takes into account the fact that, in a viable network, reactions must be capable of sustaining a steady-state flux. In order to achieve this decomposition we introduce a new concept—the reaction correlation coefficient, φ , and show that this is a logical extension of the concept of enzyme (or reaction) subsets. In addition to their application to modular decomposition, reaction correlation coefficients have a number of other interesting properties, including a convenient means for identifying disconnected subnetworks in a system and potential applications to metabolic engineering. The method computes reaction correlation coefficients from an orthonormal basis of the null-space of the stoichiometry matrix. We show that reaction correlation coefficients are uniquely defined, even though the basis of the null-space is not. Once a complete set of reaction correlation coefficients is calculated, a metabolic reaction tree can be determined through the application of standard programming techniques. Computation of the reaction correlation coefficients, and the subsequent construction of the metabolic reaction tree is readily achievable for genome-scale models using a commodity desk-top PC.