Enumerating Minimal Active Metabolic Pathways by Model Generation

DOI Web Site BIBCODE 17 References Open Access
  • Soh Takehide
    Transdisciplinary Research Integration Center
  • Inoue Katsumi
    National Institute of Informatics./Department of Informatics, The Graduate University for Advanced Studies

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  • モデル生成を用いた代謝ネットワークにおける極小活性パスウェイの列挙

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In systems biology, identifying vital functions like glycolysis from a given metabolic pathway is important to understand living organisms. In this paper, we particularly focus on the problem of enumerating minimal active pathways producing target metabolites from source metabolites. We represent the problem in propositional formulas and solve it through minimal model generation. An advantage of our method is that each solution satisfies qualitative laws of biochemical reactions. Moreover, we can calculate such solutions for a cellular scale metabolic pathway within a few seconds. In experiments, we have applied our method to a whole Escherichia coli metabolic pathway. As a result, we found a minimal set of reactions corresponding to the conventional glycolysis pathway described in a biological database EcoCyc.

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