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Abstract
Introduction
Complexity Results
Case of Several Types of Constraints
General Case of Sign-Compatible Constraints
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Computer Science

Metabolic pathway analysis in presence of biological constraints

Profile image of Philippe DaguePhilippe Dague

2020

https://doi.org/10.1101/2020.06.27.175455
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44 pages

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Abstract

Metabolic pathway analysis is a key method to study metabolism at steady state and the elementary fluxes (EFs) is one major concept allowing one to analyze the network in terms of non-decomposable pathways. The supports of the EFs contain in particular the supports of the elementary flux modes (EFMs), which are the support-minimal pathways, and EFs coincide with EFMs when the only flux constraints are given by the irreversibility of certain reactions. Practical use of both EFMs and EFs has been hampered by the combinatorial explosion of their number in large, genome-scale, systems. The EFs give the possible pathways at steady state but the real pathways are limited by biological constraints, such as thermodynamic or, more generally, kinetic constraints and regulatory constraints from the genetic network. We provide results about the mathematical structure and geometrical characterization of the solutions space in presence of such biological constraints and revisit the concept of EFM...

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