title: Metabolic flux analysis and visualization.
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 (13)C-Metabolic Flux Analysis ((13)C-MFA), both of which are frequently used to solve such underdetermined systems, and we demonstrate FBA and (13)C-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.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Toya
authors.forename: Nobuaki
authors.initials: N
authors.lastname: Kono
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Arakawa
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D049490:Systems Biology / Q000379:methods*