From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
نویسندگان
چکیده
منابع مشابه
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising fro...
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The concept of elementary flux vector is valuable in a number of applications of metabolic engineering. For instance, in metabolic flux analysis, each admissible flux vector can be expressed as a non-negative linear combination of a small number of elementary flux vectors. However a critical issue concerns the total number of elementary flux vectors which may be huge because it combinatorially ...
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UNLABELLED : Elementary flux modes (EFMs) are important structural tools for the analysis of metabolic networks. It is known that many topologically feasible EFMs are biologically irrelevant. Therefore, tools are needed to find the relevant ones. We present thermodynamic tEFM analysis (tEFMA) which uses the cellular metabolome to avoid the enumeration of thermodynamically infeasible EFMs. Speci...
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Elementary flux mode analysis (EFM analysis) is an important method in the study of biochemical pathways. However, the computation of EFMs is limited to small and medium size metabolic networks due to a combinatorial explosion in their number in larger networks. Additionally, the existing tools to compute EFMs require to enumerate all EFMs before selecting those of interest. The method presente...
متن کاملRobust generation of elementary flux modes
Elementary flux modes (EFMs) are vectors defined from a metabolic reaction network, giving the connections between substrates and products. EFMs-based metabolic flux analysis (MFA) estimates the flux over each EFM from external flux measurements through least-squares data fitting. In previous work we presented an optimization method of column generation type that facilitates EFMs-based MFA when...
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ژورنال
عنوان ژورنال: PLOS Computational Biology
سال: 2017
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1005409