Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Metabolic Pathway Analysis

  • Meghna Rajvanshi
  • Kareenhalli V. Venkatesh
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1083



Metabolic pathway analysis, a methodology used in  metabolic pathway modeling, assesses inherent network properties and identifies meaningful structural and functional units in the metabolic networks (Klamt et al. 2003). Elementary flux modes (EFMs) and extreme pathways are the most promising approaches in MPA which is based on Convex Analysis. MPA can be used to study meaningful pathways (routes) and flexibility in metabolic networks. It is feasible to identify futile cycles and all (sub) optimal pathways related to the production of a metabolite in the network. The main applications of these approaches include metabolic network analysis, and analysis of  robustness and identification of target genes in metabolic engineering.


Elementary Flux Modes (EFMs)

An EFM is defined as a minimal set of enzymes (participating reactions) that function at steady state with irreversible reactions proceeding in appropriate...
This is a preview of subscription content, log in to check access.


  1. Gayen K, Venkatesh KV (2006) Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum. BMC Bioinformatics 7. doi:445 10.1186/1471-2105-7-445Google Scholar
  2. Klamt S, Gilles ED (2004) Minimal cut sets in biochemical reaction networks. Bioinformatics 20(2):226–234. doi:10.1093/bioinformatics/btg395CrossRefPubMedGoogle Scholar
  3. Klamt S, Jr S, Ginkel M, Gilles ED (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19(2):261–269. doi:10.1093/bioinformatics/19.2.261CrossRefPubMedGoogle Scholar
  4. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO (2004) Comparison of network-based pathway analysis methods. Trends Biotechnol 22(8):400–405CrossRefPubMedGoogle Scholar
  5. Poolman MG, Venkatesh KV, Pidcock MK, Fell DA (2004) A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus. Biotechnol Bioeng 88(5):601–612. doi:10.1002/bit.20273CrossRefPubMedGoogle Scholar
  6. Schilling CH, Letscher D, Palsson BO (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 203(3):229–248CrossRefPubMedGoogle Scholar
  7. Schuster S, Hilgetag C (1994) On elementary flux modes in biochemical reaction systems at steady state. J Biol Syst 2(2):165–182CrossRefGoogle Scholar
  8. Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420(6912):190–193CrossRefPubMedGoogle Scholar
  9. Trinh C, Wlaschin A, Srienc F (2009) Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 81(5):813–826CrossRefPubMedGoogle Scholar
  10. Wiback SJ, Mahadevan R, Palsson BO (2003) Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum. J Theor Biol 224(3):313–324CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Meghna Rajvanshi
    • 1
  • Kareenhalli V. Venkatesh
    • 1
  1. 1.Department of Chemical EngineeringIndian Institute of Technology BombayPowai, MumbaiIndia