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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism
Cong T Trinh1, Aaron Wlaschin, Friedrich Srienc
1Department of Chemical Engineering and Materials Science, University of Minnesota, 151 Amundson Hall, 421 Washington Ave SE, Minneapolis, MN 55455, USA.
Applied Microbiology and Biotechnology
|November 19, 2008
Summary
Elementary mode analysis (EMA) is a metabolic pathway analysis tool that identifies cellular phenotypes by decomposing complex metabolic networks into minimal pathways. This approach aids in understanding cell physiology and advancing metabolic engineering strategies.
Area of Science:
- Systems Biology
- Metabolic Engineering
- Computational Biology
Background:
- Metabolic networks are highly interconnected and complex.
- Understanding the relationship between genotype and cellular phenotype is crucial.
- Existing analysis tools may not fully capture the intricacies of metabolic pathways.
Purpose of the Study:
- To provide an overview of elementary mode analysis (EMA).
- To highlight the development and applications of EMA in studying cell physiology.
- To demonstrate EMA's utility as a basis for metabolic engineering.
Main Methods:
- Decomposition of metabolic networks into elementary modes.
- Identification of minimal pathways supporting steady-state metabolism.
- Systematic characterization of cellular phenotypes, regulation, robustness, and fragility.
Main Results:
- EMA reveals unique pathways representing independent cellular physiological states.
- The analysis provides a rigorous framework for characterizing metabolic networks.
- EMA facilitates a deeper understanding of cell physiology.
Conclusions:
- Elementary mode analysis is a powerful tool for metabolic pathway analysis.
- EMA aids in understanding cell physiology and guiding metabolic engineering.
- The method offers insights into cellular robustness and fragility.
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