Improving the EFMs quality by augmenting their representativeness in LP methods
Author
Hidalgo Céspedes, José Francisco; Egea Larrosa, José Alberto; Guil Asensio, Francisco de Asís; García Carrasco, José ManuelKnowledge Area
Matemática AplicadaSponsors
Publication cost of this article was funded by the Spanish Ministerio de Economia y Competitividad (MINECO) and European Commission FEDER under grant TIN2015-66972-C5-3-Publication date
2018-11-20Publisher
BMCBibliographic Citation
Hidalgo, J.F., Egea, J.A., Guil, F. et al. Improving the EFMs quality by augmenting their representativeness in LP methods. BMC Syst Biol 12, 101 (2018). https://doi.org/10.1186/s12918-018-0619-1Peer review
SiKeywords
Metabolic networksPathways and EFMs
Representativeness and quality
Flux modes
Linear programming
Systems biology
Abstract
Background
Although cellular metabolism has been widely studied, its fully comprehension is still a challenge. A main tool for this study is the analysis of meaningful pieces of knowledge called modes and, in particular, specially interesting classes of modes such as pathways and Elementary Flux Modes (EFMs). Its study often has to deal with issues such as the appearance of infeasibilities or the difficulty of finding representative enough sets of modes that are free of repetitions. Mode extraction methods usually incorporate strategies devoted to mitigate this phenomena but they still get a high ratio of repetitions in the set of solutions.
Results
This paper presents a proposal to improve the representativeness of the full set of metabolic reactions in the set of computed modes by penalizing the eventual high frequency of occurrence of some reactions during the extraction. This strategy can be applied to any linear programming based extraction existent method.
Conclusions
Our ...
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