Minimal cut sets in biochemical reaction networks.

@article{citeulike:300733, abstract = {MOTIVATION: Structural studies of metabolic networks yield deeper insight into topology, functionality and capabilities of the metabolisms of different organisms. Here, we address the analysis of potential failure modes in metabolic networks whose occurrence will render the network structurally incapable of performing certain functions. Such studies will help to identify crucial parts in the network structure and to find suitable targets for repressing undesired metabolic functions. RESULTS: We introduce the concept of minimal cut sets for biochemical networks. A minimal cut set (MCS) is a minimal (irreducible) set of reactions in the network whose inactivation will definitely lead to a failure in certain network functions. We present an algorithm which enables the computation of the MCSs in a given network related to user-defined objective reactions. This algorithm operates on elementary modes. A number of potential applications are outlined, including network verifications, phenotype predictions, assessing structural robustness and fragility, metabolic flux analysis and target identification in drug discovery. Applications are illustrated by the MCSs in the central metabolism of Escherichia coli for growth on different substrates. AVAILABILITY: Computation and analysis of MCSs is an additional feature of the FluxAnalyzer (freely available for academic users upon request, special contracts for industrial companies; see web page below). Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer}, address = {Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr.1, D-39106 Magdeburg, Germany. klamt@mpi-magdeburg.mpg.de}, author = {Klamt, S. and Gilles, E. D. }, citeulike-article-id = {300733}, doi = {http://dx.doi.org/10.1093/bioinformatics/btg395}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {min\_cutset}, month = {January}, number = {2}, pages = {226--234}, posted-at = {2008-07-25 16:12:41}, priority = {2}, title = {Minimal cut sets in biochemical reaction networks.}, url = {http://dx.doi.org/10.1093/bioinformatics/btg395}, volume = {20}, year = {2004} }

TY - JOUR ID - citeulike:300733 L3 - citeulike-article-id:300733 TI - Minimal cut sets in biochemical reaction networks. JF - Bioinformatics VL - 20 IS - 2 SP - 226 EP - 234 AD - Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr.1, D-39106 Magdeburg, Germany. klamt@mpi-magdeburg.mpg.de SN - 1367-4803 N2 - MOTIVATION: Structural studies of metabolic networks yield deeper insight into topology, functionality and capabilities of the metabolisms of different organisms. Here, we address the analysis of potential failure modes in metabolic networks whose occurrence will render the network structurally incapable of performing certain functions. Such studies will help to identify crucial parts in the network structure and to find suitable targets for repressing undesired metabolic functions. RESULTS: We introduce the concept of minimal cut sets for biochemical networks. A minimal cut set (MCS) is a minimal (irreducible) set of reactions in the network whose inactivation will definitely lead to a failure in certain network functions. We present an algorithm which enables the computation of the MCSs in a given network related to user-defined objective reactions. This algorithm operates on elementary modes. A number of potential applications are outlined, including network verifications, phenotype predictions, assessing structural robustness and fragility, metabolic flux analysis and target identification in drug discovery. Applications are illustrated by the MCSs in the central metabolism of Escherichia coli for growth on different substrates. AVAILABILITY: Computation and analysis of MCSs is an additional feature of the FluxAnalyzer (freely available for academic users upon request, special contracts for industrial companies; see web page below). Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer KW - min_cutset AU - Klamt, S AU - Gilles, ED PY - 2004/01/22/ UR - http://dx.doi.org/10.1093/bioinformatics/btg395 ER -