A Lattice-Theoretic Framework for Metabolic Pathway Analysis
Please always quote using this URN:urn:nbn:de:0296-matheon-12067
- Constraint-based analysis of metabolic networks has become a widely used approach in computational systems biology. In the simplest form, a metabolic network is represented by a stoichiometric matrix and thermodynamic information on the irreversibility of certain reactions. Then one studies the set of all steady-state flux vectors satisfying these stoichiometric and thermodynamic constraints. We introduce a new lattice-theoretic framework for the computational analysis of metabolic networks, which focuses on the support of the flux vectors, i.e., we consider only the qualitative information whether or not a certain reaction is active, but not its specific flux rate. Our lattice-theoretic view includes classical metabolic pathway analysis as a special case, but turns out to be much more flexible and general, with a wide range of possible applications. We show how important concepts from metabolic pathway analysis, such as blocked reactions, flux coupling, or elementary modes, can be generalized to arbitrary lattice-based models. We develop corresponding general algorithms and present a number of computational results.
Author: | Yaron A. B. Goldstein, Alexander Bockmayr |
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URN: | urn:nbn:de:0296-matheon-12067 |
Referee: | Peter Deuflhard |
Document Type: | Preprint, Research Center Matheon |
Language: | English |
Date of first Publication: | 2013/04/23 |
Release Date: | 2013/04/23 |
Tag: | constraint-based analysis; lattice theory; metabolic networks, |
Institute: | Research Center Matheon |
Freie Universität Berlin | |
MSC-Classification: | 92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C42 Systems biology, networks |
Preprint Number: | 1006 |