Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection
| Autor: | Alexander Bockmayr, Tanguy Riou, Annika Röhl |
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| Rok vydání: | 2018 |
| Předmět: |
Statistics and Probability
Computer science Genome scale Metabolic network Models Biological Biochemistry Set (abstract data type) 03 medical and health sciences Escherichia coli Projection (set theory) Molecular Biology 030304 developmental biology 0303 health sciences Genome 030302 biochemistry & molecular biology Computational Biology Computer Science Applications Computational Mathematics Oriented matroid Computational Theory and Mathematics Cone (topology) Algorithm Flux (metabolism) Algorithms Metabolic Networks and Pathways Software |
| Zdroj: | Bioinformatics. 35:2618-2625 |
| ISSN: | 1460-2059 1367-4803 |
| DOI: | 10.1093/bioinformatics/bty1027 |
| Popis: | Motivation Minimal cut sets (MCSs) for metabolic networks are sets of reactions which, if they are removed from the network, prevent a target reaction from carrying flux. To compute MCSs different methods exist, which may fail to find sufficiently many MCSs for larger genome-scale networks. Results Here we introduce irreversible minimal cut sets (iMCSs). These are MCSs that consist of irreversible reactions only. The advantage of iMCSs is that they can be computed by projecting the flux cone of the metabolic network on the set of irreversible reactions, which usually leads to a smaller cone. Using oriented matroid theory, we show how the projected cone can be computed efficiently and how this can be applied to find iMCSs even in large genome-scale networks. Availability and implementation Software is freely available at https://sourceforge.net/projects/irreversibleminimalcutsets/. Supplementary information Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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