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From Metabolic Reactions to Networks and Pathways

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Bacterial Molecular Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 804))

Abstract

Enzymatic reactions form a hypergraph structure and their translation into a graph structure accompanies an information loss. This chapter introduces well-known topological transformations from metabolic reactions to a graph, and discusses their advantages and disadvantages. Also discussed is the legitimacy of defining cofactors or currency metabolites, and suitable application area of each representation.

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Acknowledgments

The author thanks the editors and reviewers for valuable comments. This work is supported by JST-BIRD and Grant-in-Aid for Scientific Research on Priority Areas “Systems Genomics” from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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Authors and Affiliations

  1. Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan

    Masanori Arita

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  1. Masanori Arita
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Correspondence to Masanori Arita .

Editor information

Editors and Affiliations

  1. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, bd. du Triomphe, Bruxelles, 1050, Belgium

    Jacques van Helden

  2. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bvd. du Triomphe, Bruxelles, 1050, Belgium

    Ariane Toussaint

  3. INSERM 1024, Institut de Biologie de l'Ecole Normale, rue d'Ulm 46, Paris, 75230, France

    Denis Thieffry

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Arita, M. (2012). From Metabolic Reactions to Networks and Pathways. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-361-5_6

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  • DOI: https://doi.org/10.1007/978-1-61779-361-5_6

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-360-8

  • Online ISBN: 978-1-61779-361-5

  • eBook Packages: Springer Protocols

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