Integration of metabolomics data into metabolic networks

Frontiers in Plant Science
Nadine TöpferZoran Nikoloski

Abstract

Metabolite levels together with their corresponding metabolic fluxes are integrative outcomes of biochemical transformations and regulatory processes and they can be used to characterize the response of biological systems to genetic and/or environmental changes. However, while changes in transcript or to some extent protein levels can usually be traced back to one or several responsible genes, changes in fluxes and particularly changes in metabolite levels do not follow such rationale and are often the outcome of complex interactions of several components. The increasing quality and coverage of metabolomics technologies have fostered the development of computational approaches for integrating metabolic read-outs with large-scale models to predict the physiological state of a system. Constraint-based approaches, relying on the stoichiometry of the considered reactions, provide a modeling framework amenable to analyses of large-scale systems and to the integration of high-throughput data. Here we review the existing approaches that integrate metabolomics data in variants of constrained-based approaches to refine model reconstructions, to constrain flux predictions in metabolic models, and to relate network structural properties t...Continue Reading

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Citations

Sep 27, 2016·Applied & Translational Genomics·Jaeyun SungNicholas Chia
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Jan 13, 2016·FEMS Microbiology Letters·Satyakam DashCostas D Maranas
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Nov 2, 2019·International Journal of Molecular Sciences·Lisa FürtauerThomas Nägele
Jan 26, 2021·Biochemical Society Transactions·Nadine Töpfer
Jul 21, 2016·Journal of Proteome Research·Edoardo SaccentiClaudio Luchinat
Sep 3, 2021·Computational and Structural Biotechnology Journal·Ankur SahuNadine Töpfer

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Methods Mentioned

BETA
gene knockouts
gene knock out

Software Mentioned

Flux
Integrative Discrepancy Minimizer Flux Balance Analysis
OCFE
Temporal Expression - based Analysis of Metabolism ( TEAM )
ROOM
Dynamic Flux Balance Analysis ( DFBA )
MOMA
TREM
IOMA Integrative Omics - Metabolic Analysis
mTOW

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