Comparison of metabolite production capability indices generated by network analysis methods
| Autor: | Masaru Tomita, Shinichi Kikuchi, Masahiro Sugimoto, Yoshiaki Ohashi, Seira Nakamura, Mineo Morohashi, Kyota Ishii |
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| Rok vydání: | 2008 |
| Předmět: |
Statistics and Probability
Biochemical Phenomena Applied Mathematics Metabolite Cobra General Medicine Computational biology Biology computer.software_genre Pathway analysis Biochemistry Models Biological General Biochemistry Genetics and Molecular Biology Biological pathway Constraint (information theory) chemistry.chemical_compound Metabolic pathway chemistry Modeling and Simulation Production (economics) Computer Simulation Data mining computer computer.programming_language Network analysis |
| Zdroj: | Biosystems. 91:166-170 |
| ISSN: | 0303-2647 |
| DOI: | 10.1016/j.biosystems.2007.08.010 |
| Popis: | A framework of constraint-based reconstruction and analysis (COBRA) is used for modeling large-scale metabolic networks. In COBRA, extreme pathway and optimization analyses are commonly used to study the properties of networks. While the results of both methods are completely consistent, extreme pathway analysis is considered to be better because of its wider representational ability. In this study, we assessed these two methods by computational knockout experiments. We examined a simple pathway model and found that the extreme pathway method led to misguided conclusions in specific cases, while optimization analysis calculated the correct knockout effects. We also investigated the Escherichia coli metabolic pathway model, and found that these methods result in inconsistent interpretations of the network properties. In conclusion it has been claimed that these two methods result in the same producible metabolites, but we found a difference in individual results for a biological pathway. Our results could provide helpful guidance for when to use the methods, particularly extreme pathway analysis. |
| Databáze: | OpenAIRE |
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