Metabolic flux analysis and visualization

Yoshihiro Toya, Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

One of the ultimate goals of systems biology research is to obtain a comprehensive understanding of the control mechanisms of complex cellular metabolisms. Metabolic Flux Analysis (MFA) is a important method for the quantitative estimation of intracellular metabolic flows through metabolic pathways and the elucidation of cellular physiology. The primary challenge in the use of MFA is that many biological networks are underdetermined systems; it is therefore difficult to narrow down the solution space from the stoichiometric constraints alone. In this tutorial, we present an overview of Flux Balance Analysis (FBA) and 13C-Metabolic Flux Analysis ( 13C-MFA), both of which are frequently used to solve such underdetermined systems, and we demonstrate FBA and 13C-MFA using the genome-scale model and the central carbon metabolism model, respectively. Furthermore, because such comprehensive study of intracellular fluxes is inherently complex, we subsequently introduce various pathway mapping and visualization tools to facilitate understanding of these data in the context of the pathways. Specific visualization of MFA results using the BioCyc Omics Viewer and Pathway Projector are shown as illustrative examples.

Original languageEnglish
Pages (from-to)3313-3323
Number of pages11
JournalJournal of Proteome Research
Volume10
Issue number8
DOIs
Publication statusPublished - 2011 Aug 5

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Metabolic Flux Analysis
Visualization
Fluxes
Metabolism
Systems Biology
Metabolic Networks and Pathways
Carbon
Genome
Physiology
Research
Genes

Keywords

  • C-Metabolic Flux Analysis
  • Flux Balance Analysis
  • genome-scale model
  • Pathway Projector

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Metabolic flux analysis and visualization. / Toya, Yoshihiro; Kono, Nobuaki; Arakawa, Kazuharu; Tomita, Masaru.

In: Journal of Proteome Research, Vol. 10, No. 8, 05.08.2011, p. 3313-3323.

Research output: Contribution to journalArticle

Toya, Yoshihiro ; Kono, Nobuaki ; Arakawa, Kazuharu ; Tomita, Masaru. / Metabolic flux analysis and visualization. In: Journal of Proteome Research. 2011 ; Vol. 10, No. 8. pp. 3313-3323.
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