Skip to main content
SpringerLink
Log in

Complex networks theory for analyzing metabolic networks

  • Review
  • Published:
Chinese Science Bulletin

Abstract

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Kanehisa M. Post-Genome Informatics. Oxford: Oxford Univ Press, 2000

    Google Scholar 

  2. Erdös P, Rényi A. On random graphs. Publ Math Debrecen, 1959, 6: 290–297

    Google Scholar 

  3. Watts D J, Strogatz S H. Collective dynamics of ’small-world’ networks. Nature, 1998, 393: 440–442

    Article  Google Scholar 

  4. Barabasi A L, Albert R. Emergence of scaling in random networks. Science, 1999, 286: 509–512

    Article  Google Scholar 

  5. Jeong H, Tombor B, Albert R, et al. The large-scale organization of metabolic networks. Nature, 2000, 407: 651–654

    Article  Google Scholar 

  6. Goto S, Nishioka T, Kanehisa M. LIGAND: Chemical database for enzyme reactions. Bioinformatics, 1998, 14: 591–599

    Article  Google Scholar 

  7. Bairoch A. The ENZYME data bank in 1995. Nucleic Acids Res, 1996, 24: 221–222

    Article  Google Scholar 

  8. Nakao M, Bono H, Kawashima S, et al. Genome-scale gene expression analysis and pathway reconstruction in KEGG. Genome Informatics, 1999, 10: 94–103

    Google Scholar 

  9. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 2000, 28: 27–30

    Article  Google Scholar 

  10. Karp P D, Krummenacker M, Paley S, et al. Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol, 1999, 17: 275–281

    Article  Google Scholar 

  11. Karp P D. Pathway databases: A case study in computational symbolic theories. Science, 2001, 293: 2040–2044

    Article  Google Scholar 

  12. Overbeek R, Larsen N, Pusch G D, et al. WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res, 2000, 28: 123–125

    Article  Google Scholar 

  13. Schuster S, Fell D, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnol, 2000, 18: 326–332

    Article  Google Scholar 

  14. Wagner A, Fell D A. The small world inside large metabolic networks. Proc R Soc Lond B, 2001, 268: 1803–1810

    Article  Google Scholar 

  15. Ravasz E, Somera A L, Mongru D A, et al. Hierarchical organization of modularity in metabolic networks. Science, 2002, 297: 1551–1556

    Article  Google Scholar 

  16. Ma H W, Zeng A P. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics, 2003, 19: 270–277

    Article  Google Scholar 

  17. Ma H W, Zeng A P. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics, 2003, 19: 1423–1430

    Article  Google Scholar 

  18. Guimera R, Amaral L A N. Functional cartography of complex metabolic networks. Nature, 2005, 433: 895–900

    Article  Google Scholar 

  19. Ma H W, Zhao X M, Yuan Y J, et al. Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph., Bioinformatics, 2004, 20: 1870–1876

    Article  Google Scholar 

  20. Horne A B, Hodgman T C, Spence H D, et al. Constructing an enzyme-centric view of metabolism. Bioinformatics, 2004, 20: 2050–2055

    Article  Google Scholar 

  21. Gagneur J, Jackson D B, Casari G. Hierarchical analysis of dependency in metabolic networks. Bioinformatics, 2003, 19: 1027–1034

    Article  Google Scholar 

  22. Lemke N, Herédia F, Barcellos C K, et al. Essentiality and damage in metabolic networks. Bioinformatics, 2004, 20: 115–119

    Article  Google Scholar 

  23. Arita M. The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci USA, 2004, 101: 1543–1547

    Article  Google Scholar 

  24. Broder A, Kumar R, Maghoul F, et al. Graph structure in the web. Comput Netw, 2000, 33: 309–320

    Article  Google Scholar 

  25. Faloutsos M, Faloutsos P, Faloutsos C. On power-law relationships of the internet topology. Comp Comm Rev, 1999, 29: 251–262

    Article  Google Scholar 

  26. Ravasz E, Barabási A L. Hierarchical organization in complex networks. Phys Rev E, 2003, 67: 026112

    Google Scholar 

  27. Hartwell L H, Hopfield J J, Leibler S, et al. From molecular to modular cell biology. Nature, 1999, 402: C47–C51

    Article  Google Scholar 

  28. Lipson H, Pollack J B, Suh N P. On the origin of modular variation. Evolution, 2002, 56: 1549–1556.

    Google Scholar 

  29. Papin J A, Price N D, Palsson B O. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res, 2002, 12: 1889–1900

    Article  Google Scholar 

  30. Stelling J, Klamt S, Bettenbrock K, et al. Metabolic network structure determines key aspects of functionality and regulation. Nature, 2002, 420: 190–193

    Article  Google Scholar 

  31. Schilling C H, Palsson B O. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol, 2000, 203: 249–283

    Article  Google Scholar 

  32. Schuster S, Pfeiffer T, Moldenhauer F, et al. Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics, 2002, 18: 351–361

    Article  Google Scholar 

  33. Holme P, Huss M, Jeong H. Subnetwork hierarchies of biochemical pathways. Bioinformatics, 2003, 19: 532–538

    Article  Google Scholar 

  34. Schuster R, Holzhütter H G. Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations: Application to enzyme deficiencies of red blood cells. Eur J Biochem, 1995, 229: 403–418

    Article  Google Scholar 

  35. Martinov M V, Plotnikov A G, Vitvitsky V M, et al. Deficiencies of glycolytic enzymes as a possible cause of hemolytic anemia. Biochim Biophys Acta, 2000, 1474: 75–87

    Google Scholar 

  36. Bakker B M, Mensonides F I C, Teusink B, et al. Compartmentation protects trypanosomes from the dangerous design of glycolysis. Proc Natl Acad Sci USA, 2000, 97: 2087–2092

    Article  Google Scholar 

  37. Wagner C. Systembiologie gegen Parasiten. BioWorld, 2004, 9: 2–4

    Google Scholar 

  38. Kitano H. Biological robustness. Nature Rev Genetic, 2004, 5: 826–837

    Article  Google Scholar 

  39. Stelling J, Sauer U, Szallasi Z, et al. Robustness of cellular functions. Cell, 2004, 118: 675–685

    Article  Google Scholar 

  40. Albert R, Jeong H, Barabasi A L. Error and attack tolerance of complex networks. Nature, 2000, 406: 378–382

    Article  Google Scholar 

  41. Mahadevan R, Palsson B O. Properties of metabolic networks: Structure versus function. Biophysical J, 2005, 88: L7–L9

    Article  Google Scholar 

  42. Samal A, Singh S, Giri V, et al. Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinfor, 2006, 7: 118

    Article  Google Scholar 

  43. Palumbo M C, Colosimo A, Giuliani A, et al. Functional essentiality from topology features in metabolic networks: A case study in yeast. FEBS Lett, 2005, 579: 4642–4646

    Article  Google Scholar 

  44. Mombach J C M, Lemke N, Silva N M, et al. Bioinformatics analysis of mycoplasma metabolism: Important enzymes, metabolic similarities, and redundancy. Comput Biol Med, 2006, 36(5): 542–552

    Article  Google Scholar 

  45. Wuchty S, Ravasz E, Barabási A L. The architecture of biological networks. In: Deisboeck T S, Kresh J Y, Kepler T B, eds. Complex Systems in Biomedicine. New York: Kluwer Academic Publishing, 2003

    Google Scholar 

  46. Barabasi A L, Oltvai Z N. Network biology: Understanding the cells’s functional organization. Nature Rev Genetics, 2004, 5: 101–113

    Article  Google Scholar 

  47. Oltvai Z N, Barabási A L. Life’s complexity pyramid. Science, 2002, 298: 763–764

    Article  Google Scholar 

  48. Newman M E J. Mixing patterns in networks. Phys Rev E, 2003, 67(2 Pt2): 026126

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China

    Zhao Jing, Luo Jianhua & Li Yixue

  2. Shanghai Center for Bioinformation and Technology, Shanghai, 200235, China

    Zhao Jing, Yu Hong, Cao Z. W. & Li Yixue

  3. Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Li Yixue

  4. Department of mathematics, Logistical Engineering University, Chongqing, 400016, China

    Zhao Jing

Authors
  1. Zhao Jing
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu Hong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Luo Jianhua
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cao Z. W.
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Li Yixue
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Cao Z. W. or Li Yixue.

About this article

Cite this article

Zhao, J., Yu, H., Luo, J. et al. Complex networks theory for analyzing metabolic networks. CHINESE SCI BULL 51, 1529–1537 (2006). https://doi.org/10.1007/s11434-006-2015-2

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11434-006-2015-2

Keywords

Search

Navigation