Comparison of metabolite production capability indices generated by network analysis methods

Kyota Ishii, Seira Nakamura, Mineo Morohashi, Masahiro Sugimoto, Yoshiaki Ohashi, Shinichi Kikuchi, Masaru Tomita

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

A framework of constraint-based reconstruction and analysis (COBRA) is used for modeling large-scale metabolic networks. In COBRA, extreme pathway and optimization analyses are commonly used to study the properties of networks. While the results of both methods are completely consistent, extreme pathway analysis is considered to be better because of its wider representational ability. In this study, we assessed these two methods by computational knockout experiments. We examined a simple pathway model and found that the extreme pathway method led to misguided conclusions in specific cases, while optimization analysis calculated the correct knockout effects. We also investigated the Escherichia coli metabolic pathway model, and found that these methods result in inconsistent interpretations of the network properties. In conclusion: it has been claimed that these two methods result in the same producible metabolites, but we found a difference in individual results for a biological pathway. Our results could provide helpful guidance for when to use the methods, particularly extreme pathway analysis.

Original languageEnglish
Pages (from-to)166-170
Number of pages5
JournalBioSystems
Volume91
Issue number1
DOIs
Publication statusPublished - 2008 Jan

Fingerprint

network analysis
Network Analysis
Electric network analysis
Metabolites
Pathway
metabolite
metabolites
Escherichia coli
Extremes
Metabolic Networks and Pathways
methodology
Aptitude
Experiments
Metabolic Network
Optimization
Individuality
biochemical pathways
comparison
index
method

Keywords

  • A framework of constraint-based reconstruction and analysis
  • Biological pathway
  • Knockout analysis

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Biotechnology
  • Drug Discovery

Cite this

Comparison of metabolite production capability indices generated by network analysis methods. / Ishii, Kyota; Nakamura, Seira; Morohashi, Mineo; Sugimoto, Masahiro; Ohashi, Yoshiaki; Kikuchi, Shinichi; Tomita, Masaru.

In: BioSystems, Vol. 91, No. 1, 01.2008, p. 166-170.

Research output: Contribution to journalArticle

Ishii, K, Nakamura, S, Morohashi, M, Sugimoto, M, Ohashi, Y, Kikuchi, S & Tomita, M 2008, 'Comparison of metabolite production capability indices generated by network analysis methods', BioSystems, vol. 91, no. 1, pp. 166-170. https://doi.org/10.1016/j.biosystems.2007.08.010
Ishii K, Nakamura S, Morohashi M, Sugimoto M, Ohashi Y, Kikuchi S et al. Comparison of metabolite production capability indices generated by network analysis methods. BioSystems. 2008 Jan;91(1):166-170. https://doi.org/10.1016/j.biosystems.2007.08.010
Ishii, Kyota ; Nakamura, Seira ; Morohashi, Mineo ; Sugimoto, Masahiro ; Ohashi, Yoshiaki ; Kikuchi, Shinichi ; Tomita, Masaru. / Comparison of metabolite production capability indices generated by network analysis methods. In: BioSystems. 2008 ; Vol. 91, No. 1. pp. 166-170.
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