Publication: On the representativeness and stability of a set of EFMs
Authors
Guil Asensio, Francisco ; Hidalgo Céspedes, José Francisco ; García Carrasco, José Manuel
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Publisher
Oxford Academic
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DOI
https://doi.org/10.1093/bioinformatics/btad356
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info:eu-repo/semantics/article
Description
©2023. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
This document is the Published, version of a Published Work that appeared in final form in Bioinformatics. To access the final edited and published work see https://doi.org/10.1093/bioinformatics/btad356
Abstract
Motivation: Elementary flux modes are a well-known tool for analyzing metabolic networks. The whole set of elementary flux modes (EFMs)
cannot be computed in most genome-scale networks due to their large cardinality. Therefore, different methods have been proposed to compute
a smaller subset of EFMs that can be used for studying the structure of the network. These latter methods pose the problem of studying the
representativeness of the calculated subset. In this article, we present a methodology to tackle this problem.
Results: We have introduced the concept of stability for a particular network parameter and its relation to the representativeness of the EFM
extraction method studied. We have also defined several metrics to study and compare the EFM biases. We have applied these techniques to
compare the relative behavior of previously proposed methods in two case studies. Furthermore, we have presented a new method for the EFM
computation (PiEFM), which is more stable (less biased) than previous ones, has suitable representativeness measures, and exhibits better
variability in the extracted EFMs
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Citation
Bioinformatics, 2023, 39(6), btad356
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