抄録
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.
| 元の言語 | English |
|---|---|
| ページ（範囲） | 3313-3323 |
| ページ数 | 11 |
| ジャーナル | Journal of Proteome Research |
| 巻 | 10 |
| 発行部数 | 8 |
| DOI | |
| 出版物ステータス | Published - 2011 8 5 |
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ASJC Scopus subject areas
- Biochemistry
- Chemistry(all)
これを引用
Metabolic flux analysis and visualization. / Toya, Yoshihiro; Kono, Nobuaki; Arakawa, Kazuharu; Tomita, Masaru.
：: Journal of Proteome Research, 巻 10, 番号 8, 05.08.2011, p. 3313-3323.研究成果: Article
}
TY - JOUR
T1 - Metabolic flux analysis and visualization
AU - Toya, Yoshihiro
AU - Kono, Nobuaki
AU - Arakawa, Kazuharu
AU - Tomita, Masaru
PY - 2011/8/5
Y1 - 2011/8/5
N2 - 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.
AB - 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.
KW - C-Metabolic Flux Analysis
KW - Flux Balance Analysis
KW - genome-scale model
KW - Pathway Projector
UR - http://www.scopus.com/inward/record.url?scp=79961221205&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79961221205&partnerID=8YFLogxK
U2 - 10.1021/pr2002885
DO - 10.1021/pr2002885
M3 - Article
C2 - 21815690
AN - SCOPUS:79961221205
VL - 10
SP - 3313
EP - 3323
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
IS - 8
ER -