Finding minimal generating set for metabolic network with reversible pathways

Jevremovic, Dimitrije; Boley, Daniel

doi:10.1016/j.biosystems.2013.02.003

“…We prove that all generating flux vectors obtained by our approach are EFMs. [18] only mention that the minimum set of EFMs is not unique. Here we discuss this issue in a systematic way and show how to obtain different MEMo's by splitting different sets of reversible reactions.…”

Section: Minimal Generating Setmentioning

confidence: 99%

“…The biological relevance of the MEMos has to be further investigated. The need of having smaller sets of generating flux vectors has been addressed by various papers [1,9,18,20,35,40]. We expect that MEMos give rise to new opportunities for analysing large genome-scale metabolic networks.…”

Section: Conclusion and Further Workmentioning

confidence: 99%

Finding MEMo: minimum sets of elementary flux modes

Röhl

¹

,

Bockmayr

²

2019

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Metabolic network reconstructions are widely used in computational systems biology for in silico studies of cellular metabolism. A common approach to analyse these models are elementary flux modes (EFMs), which correspond to minimal functional units in the network. Already for medium-sized networks, it is often impossible to compute the set of all EFMs, due to their huge number. From a practical point of view, this might also not be necessary because a subset of EFMs may already be sufficient to answer relevant biological questions. In this article, we study MEMos or minimum sets of EFMs that can generate all possible steady-state behaviours of a metabolic network. The number of EFMs in a MEMo may be by several orders of magnitude smaller than the total number of EFMs. Using MEMos, we can compute generating sets of EFMs in metabolic networks where the whole set of EFMs is too large to be enumerated..

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“…Larhlimi and Bockmayr show that for each MMB there exists a corresponding EFM, but they do not consider reaction splitting and do not present a method for computing a minimal generating set consisting of EFMs only. [18] introduce a method for finding a minimum generating set of flux vectors which corresponds to a set of EFMs and therefore is a MEMo. However, their approach is different from the one introduced here.…”

Section: Extreme Pathwaysmentioning

confidence: 99%

Finding MEMo: Minimum sets of elementary flux modes

Röhl

¹

,

Bockmayr

²

2019

Preprint

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Metabolic network reconstructions are widely used in computational systems biology for in silico studies of cellular metabolism. A common approach to analyse these models are elementary flux modes (EFMs), which correspond to minimal functional units in the network. Already for medium-sized networks, it is often impossible to compute the set of all EFMs, due to their huge number. From a practical point of view, this might also not be necessary because a subset of EFMs may already be sufficient to answer relevant biological questions. In this article, we study MEMos or minimum sets of EFMs that can generate all possible steady-state behaviours of a metabolic network. The number of EFMs in a MEMo may be by several orders of magnitude smaller than the total number of EFMs. Using MEMos, we can compute generating sets of EFMs in metabolic networks where the whole set of EFMs is too large to be enumerated.

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“…An important concept to analyze the flux cone in a mathematically and biologically meaningful way are elementary flux modes (EFMs) (Schuster and Hilgetag 1994 ; Schuster et al. 2002 ), which provide an inner description of the flux cone consisting of a finite set of generating vectors (Gagneur and Klamt 2004 ; Wagner and Urbanczik 2005 ; Larhlimi and Bockmayr 2008 ; Jevremovic and Boley 2013 ). From a mathematical point of view, not all elementary flux modes are needed to describe the cone, i.e., the set of all EFMs does not form a minimal generating set, except for special cases (for example when all reactions are irreversible).…”

Section: Introductionmentioning

confidence: 99%

On the geometry of elementary flux modes

Wieder,

Henk,

Bockmayr

2023

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Elementary flux modes (EFMs) play a prominent role in the constraint-based analysis of metabolic networks. They correspond to minimal functional units of the metabolic network at steady-state and as such have been studied for almost 30 years. The set of all EFMs in a metabolic network tends to be very large and may have exponential size in the number of reactions. Hence, there is a need to elucidate the structure of this set. Here we focus on geometric properties of EFMs. We analyze the distribution of EFMs in the face lattice of the steady-state flux cone of the metabolic network and show that EFMs in the relative interior of the cone occur only in very special cases. We introduce the concept of degree of an EFM as a measure how elementary it is and study the decomposition of flux vectors and EFMs depending on their degree. Geometric analysis can help to better understand the structure of the set of EFMs, which is important from both the mathematical and the biological viewpoint.

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Finding minimal generating set for metabolic network with reversible pathways

Cited by 7 publications

References 26 publications

Finding MEMo: minimum sets of elementary flux modes

Finding MEMo: minimum sets of elementary flux modes

Finding MEMo: Minimum sets of elementary flux modes

On the geometry of elementary flux modes

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