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Bayesian metabolic flux analysis reveals intracellular flux couplings.

ABSTRACT: MOTIVATION:Metabolic flux balance analysis (FBA) is a standard tool in analyzing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place model assumptions on fluxes due to the convenience of formulating the problem as a linear programing model, while many methods do not consider the inherent uncertainty in flux estimates. RESULTS:We introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as FBA. Our experiments indicate that we can characterize the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in Clostridium acetobutylicum from 13C data than flux variability analysis. AVAILABILITY AND IMPLEMENTATION:The COBRA compatible software is available at github.com/markusheinonen/bamfa. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

PROVIDER: S-EPMC6612884 | BioStudies | 2019-01-01

REPOSITORIES: biostudies

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