CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013 vol.10 Issue No.04 - July-Aug.
Issue No.04 - July-Aug. (2013 vol.10)
Onur Seref , Dept. of Bus. Inf. Technol., Virginia Polytech. Inst. & State Univ., Blacksburg, VA, USA
J. Paul Brooks , Dept. of Stat. Sci. & Oper. Res., Virginia Commonwealth Univ., Richmond, VA, USA
Stephen S. Fong , Dept. of Chem. & Life Sci. Eng., Virginia Commonwealth Univ., Richmond, VA, USA
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.115
Genome-scale reconstructions are often used for studying relationships between fundamental components of a metabolic system. In this study, we develop a novel computational method for analyzing predicted flux distributions for metabolic reconstructions. Because chemical reactions may have multiple reactants and products, a directed hypergraph where hyperarcs may have multiple tail vertices and head vertices is a more appropriate representation of the metabolic network than a conventional network. We use this view to represent predicted flux distributions by maximum generalized flows on hypergraphs. We then demonstrate that the generalized hyperflow problem may be transformed to an equivalent network flow problem with side constraints. This transformation allows a flux to be decomposed into chains of reactions. Subsequent analysis of these chains helps to characterize active pathways in a flux distribution. Such characterizations facilitate comparisons of flux distributions for different environmental conditions. The proposed method is applied to compare predicted flux distributions for Salmonella typhimurium to study changes in metabolism that cause enhanced virulence during a space flight. The differences between flux distributions corresponding to normal and enhanced virulence states confirm previous observations concerning infection mechanisms and suggest new pathways for exploration.
network theory (graphs), biochemistry, cellular biophysics, chemical reactions, directed graphs, genomics, microorganisms, infection mechanism, flux distribution decomposition, metabolic pathway, genome-scale reconstruction, computational method, metabolic reconstructions, chemical reactions, directed hypergraph, metabolic network, generalized hyperflow problem, equivalent network flow problem, reaction chain, environmental conditions, Salmonella typhimurium, space flight, virulence states, Biochemistry, Bioinformatics, Vectors, IEEE transactions, Computational biology, Organisms, Biomass, flux balance analysis, Hypergraphs, maximum generalized hyperflow, flow decomposition, metabolic reconstruction
Onur Seref, J. Paul Brooks, Stephen S. Fong, "Decomposition of Flux Distributions into Metabolic Pathways", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 4, pp. 984-993, July-Aug. 2013, doi:10.1109/TCBB.2013.115