Properties of metabolic graphs: Biological organization or representation artifacts?

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Zhou, Wanding ^a   Nakhleh, Luay ^a  

^a Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL REACTIONS; BIOLOGICAL ORGANIZATION; CLUSTERING COEFFICIENT; GRAPH REPRESENTATION; HIERARCHICAL STRUCTURES; HYPERGRAPH REPRESENTATIONS; METABOLIC REACTIONS; TOPOLOGICAL PROPERTIES;

BIOLOGICAL SYSTEMS; ESCHERICHIA COLI; GRAPHIC METHODS; METABOLISM;

GRAPH THEORY;

ESCHERICHIA COLI;

PROTEOME;

ARTICLE; ARTIFACT; BIOLOGICAL MODEL; CLUSTER ANALYSIS; ESCHERICHIA COLI; METABOLISM; METHODOLOGY; SYSTEMS BIOLOGY;

ARTIFACTS; CLUSTER ANALYSIS; ESCHERICHIA COLI; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PROTEOME; SYSTEMS BIOLOGY;

EID: 79955511378     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-132     Document Type: Article

References (33)

1. Papin J, Hunter T, Palsson B, Subramaniam S. Reconstruction of Cellular signalling networks and analysis of their properties. Nature Reviews Molecular Cell Biology 2005, 6:99-111. 10.1038/nrm1570, 15654321.
2. Lacroix V, Cottret L, Thébault P, Sagot M. An introduction to metabolic networks and their structural analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008, 5(4):594-617.
3. Patil KR, Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Nat Acad Sci USA 2005, 102:2685-2689. 10.1073/pnas.0406811102, 549453, 15710883.
4. Fell DA, Wagner A. The small world of metabolism. Nature Biotechnology 2000, 18(11):1121-1122. [PMID: 11062388], 10.1038/81025, 11062388.
5. Wagner A, Fell DA. The small world inside large metabolic networks. Proceedings of the Royal Society of London. Series B: Biological Sciences 2001, 268(1478):1803-1810. 10.1098/rspb.2001.1711, 1088812, 11522199.
6. Ma H, Zeng A. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19(11):1423-1430. 10.1093/bioinformatics/btg177, 12874056.
7. Jeong H, Tombor B, Albert R, Oltvai Z, Barabási A. The large-scale organization of metabolic networks. Nature 2000, 407:651-654. 10.1038/35036627, 11034217.
8. Arita M. The metabolic network of Escherichia coli is not small. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(6):1543-1547. 10.1073/pnas.0306458101, 341771, 14757824.
9. Klamt S, Haus UU, Theis F. Hypergraphs and Cellular Networks. PLoS Comput Biol 2009, 5(5):e1000385. 10.1371/journal.pcbi.1000385, 2673028, 19478865.
10. Berge C. Graphs and hypergraphs. English, (Amsterdam, New York): North-Holland Pub. Co., American Elsevier Pub. Co., xiv, 528 p. edition 1976 , http://openlibrary.org/b/OL14545454M/Graphs-and-hypergraphs
11. Berge C. Hypergraphs 1989, Elsevier.
12. Holme P. Model validation of simple-graph representations of metabolism. Journal of The Royal Society Interface 2009, 6(40):1027-1034.
13. Forst CV, Flamm C, Hofacker IL, Stadler PF. Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics 2006, 7:67. 10.1186/1471-2105-7-67, 1475643, 16478540.
14. Mithani A, Preston GM, Hein J. Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. Bioinformatics 2009, 25(14):1831-1832. 10.1093/bioinformatics/btp269, 19398450.
15. Haus U, Klamt S, Stephen T. Computing knock-out strategies in metabolic networks. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 2008, 15(3):259-268., http://www.ncbi.nlm.nih.gov/pubmed/18331197
16. Handorf T, Ebenhöh O, Heinrich R. Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution. Journal of Molecular Evolution 2005, 61(4):498-512. 10.1007/s00239-005-0027-1, 16155745.
17. Ay F, Kahveci T, DE Crécy-Lagard V. A fast and accurate algorithm for comparative analysis of metabolic pathways. Journal of bioinformatics and computational biology 2009, 7(3):389. 10.1142/S0219720009004163, 19507283.
18. Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60(10):3724-3731. 201879, 7986045.
19. Zevedei-Oancea I, Schuster S. Topological analysis of metabolic networks based on Petri net theory. In silico biology 2003, 3(3):323-345.
20. Hu Z, Mellor J, Wu J, Kanehisa M, Stuart J, DeLisi C. Towards zoomable multidimensional maps of the cell. Nature Biotechnology 2007, 25(5):547-554. 10.1038/nbt1304, 17483841.
21. Bertault F, Eades P. Drawing Hypergraphs in the Subset Standard (Short demo Paper). Graph Drawing 2001, 1984:45-76., http://www.springerlink.com/content/jmrt8cnw847n0b72/
22. Gallo G, Longo G, Pallottino S, Nguyen S. Directed hypergraphs and applications. Discrete Appl Math 1993, 42(2-3):177-201.
23. Nacher J, Ueda N, Yamada T, Kanehisa M, Akutsu T. Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics 2004, 5:207. 10.1186/1471-2105-5-207, 545960, 15617578.
24. Estrada E, Rodríguez-Velázquez JA. Subgraph centrality and clustering in complex hyper-networks. Physica A: Statistical Mechanics and its Applications 2006, 364:581-594.
25. Erdös P, Rényi A. On random graphs. Publ Math 1959, Debrecen 6:290-297.
26. Barabasi A, Albert R. Emergence of Scaling in Random Networks. Science 1999, 286(5439):509-512. 10.1126/science.286.5439.509, 10521342.
27. Lynch M. The evolution of genetic networks by non-adaptive processes. Nature Reviews Genetics 2007, 8(10):803-813.
28. Wagner A. Neutralism and selectionism: a network-based reconciliation. Nature Reviews Genetics 2008, 9(12):965-974.
29. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabàsi A. Hierarchical Organization of Modularity in Metabolic Networks. Science 2002, 297(5586):1551-1555. 10.1126/science.1073374, 12202830.
30. Nacher JC, Ueda N, Yamada T, Kanehisa M, Akutsu T. Study on the clustering coefficients in metabolic network using a hierarchical framework. International workshop on bioinformatics and systems biology 2004, 34-35., http://www.jsbi.org/pdfs/journal1/IBSB04/IBSB04P010.pdf
31. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucl Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
32. Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998, 393(6684):440-442. 10.1038/30918, 9623998.
33. Barrat A, Weigt M. On the properties of small-world network models. The European Physical Journal B - Condensed Matter and Complex Systems 2000, 13(3):547-560., http://www.springerlink.com/content/h34804169l475201