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Transactions on Petri Nets and Other Models of Concurrency VIII pp 1–23Cite as

Comparing Metabolic Pathways through Reactions and Potential Fluxes

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Part of the Lecture Notes in Computer Science book series (TOPNOC,volume 8100)

Abstract

Comparison of metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when studying diseases and in drugs engineering. In the literature many techniques have been proposed to compare metabolic pathways. Most of them focus on structural aspects, while behavioural or functional aspects are generally not considered. In this paper we propose a new method for comparing metabolic pathways of different organisms based on a similarity measure which considers both homology of reactions and functional aspects of the pathways. The latter are captured by relying on a Petri net representation of the pathways and comparing the corresponding T-invariant bases, which represent minimal subsets of reactions that can operate at a steady state. A prototype tool, CoMeta, implements this approach and allows us to test and validate our proposal. Some experiments with CoMeta are presented.

Keywords

  • Metabolic Pathway
  • Metabolic Network
  • Glycolysis Pathway
  • Stoichiometric Matrix
  • Full Network

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Author information

Authors and Affiliations

  1. Dipartimento di Matematica, Università di Padova, Italy

    Paolo Baldan

  2. DAIS, Università Ca’ Foscari Venezia, Italy

    Nicoletta Cocco, Federica Giummolè & Marta Simeoni

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  1. Paolo Baldan
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  2. Nicoletta Cocco
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  3. Federica Giummolè
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  4. Marta Simeoni
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Editors and Affiliations

  1. School of Computing Science, Newcastle University, NE1 7RU, Newcastle upon Tyne, UK

    Maciej Koutny

  2. Department of Mathematics and Computer Science, Eindhoven University of Technology, 5600, Eindhoven, MB, The Netherlands

    Wil M. P. van der Aalst

  3. School of Electrical, Electronic and Computer Engineering, Newcastle University, NE1 7RU, Newcastle upon Tyne, UK

    Alex Yakovlev

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Baldan, P., Cocco, N., Giummolè, F., Simeoni, M. (2013). Comparing Metabolic Pathways through Reactions and Potential Fluxes. In: Koutny, M., van der Aalst, W.M.P., Yakovlev, A. (eds) Transactions on Petri Nets and Other Models of Concurrency VIII. Lecture Notes in Computer Science, vol 8100. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40465-8_1

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