A graph-based approach to analyze flux-balanced pathways in metabolic networks

Mona Arabzadeh; Morteza Saheb Zamani; Mehdi Sedighi; Sayed-Amir Marashi

doi:10.1016/j.biosystems.2017.12.001

A graph-based approach to analyze flux-balanced pathways in metabolic networks

Biosystems. 2018 Mar:165:40-51. doi: 10.1016/j.biosystems.2017.12.001. Epub 2018 Jan 12.

Authors

Mona Arabzadeh¹, Morteza Saheb Zamani², Mehdi Sedighi³, Sayed-Amir Marashi⁴

Affiliations

¹ Department of Computer Engineering and Information Technology, Amirkabir University of Technology, Tehran, Iran. Electronic address: m.arabzadeh@aut.ac.ir.
² Department of Computer Engineering and Information Technology, Amirkabir University of Technology, Tehran, Iran. Electronic address: szamani@aut.ac.ir.
³ Department of Computer Engineering and Information Technology, Amirkabir University of Technology, Tehran, Iran. Electronic address: msedighi@aut.ac.ir.
⁴ Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran. Electronic address: marashi@ut.ac.ir.

PMID: 29337084
DOI: 10.1016/j.biosystems.2017.12.001

Abstract

An elementary flux mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. The given metabolic network is mapped to the graph model and decisions for reaction inclusion can be made based on metabolites and their associated reactions. This notion makes the approach more convenient to categorize the output pathways. Implications of the proposed method on metabolic networks are discussed.

Keywords: Elementary flux mode (EFM); Graph data model; Metabolic network.

MeSH terms

Algorithms*
Computer Graphics*
Computer Simulation
Escherichia coli / metabolism*
Metabolic Flux Analysis / methods*
Metabolic Networks and Pathways*
Models, Biological*