Copying nodes versus editing links: The source of the difference between genetic regulatory networks and the WWW

Bioinformatics

Volumn 22, Issue 5, 2006, Pages 581-588

  Louzoun, Yoram ^a   Muchnik, Lev ^a   Solomon, Sorin ^b  

^a BAR ILAN UNIVERSITY   (Israel)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CATALYSIS; CONSTANTS AND COEFFICIENTS; CORRELATION ANALYSIS; FREQUENCY ANALYSIS; GENE CLUSTER; GENE DUPLICATION; GENE MUTATION; GENETIC REGULATION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; MOLECULAR DYNAMICS; ONLINE SYSTEM; PRIORITY JOURNAL; PROCESS MODEL; TIME;

EID: 33644850066     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btk030     Document Type: Article

References (46)

1. Adamic,L.A. et al. (2000) Power-law distribution of the World Wide Web. Science, 287, 2115. www.sciencemag.org.
2. Adamic,L.A. et al. (2001) Search in power-law networks. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 64, 046135.
3. Agrawal,H. (2002) Extreme self-organization in networks constructed from gene expression data. Phys. Rev. Lett., 89, 268702.
4. Albert,R. and Barabasi,A.L. (2002) Statistical mechanics of complex networks. Rev. Modern Phys., 74, 47-97.
5. Albert,R. et al. (1999) Diameter of the World Wide Web. Nature, 401, 130-131.
6. Amaral,L.A. et al. (2000) Classes of small-world networks. Proc. Natl Acad. Sci. USA, 97, 11149-11152.
7. Barabasi,A.L. and Albert,R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
8. Barrat,A. et al. (2004) The architecture of complex weighted networks. Proc. Natl Acad. Sci. USA, 101, 3747-3752.
9. Betran,E. and Long,M. (2002) Expansion of genome coding regions by acquisition of new genes. Genetica, 115, 65-80.
10. Bhan,A. et al. (2002) A duplication growth model of gene expression networks. Bioinformatics, 18, 1486-1493.
11. Blank,A. and Solomon,S. (2000) Power laws in cities population, financimarkets and Internet sites (scaling in systems with a variable number of components). Physica A, 287, 279-288.
12. Chung,F. et al. (2003) Duplication models for biological networks. J. Comput. Biol., 10, 677-687.
13. Dehal,P. et al. (2001) Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. Science, 293, 104-111.
14. Dorogovtsev,S.N. and Mendes,J.F.F. (2001) Scaling properties of scale-free, evolving networks: Continuous approach. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 63, 1-18.
15. Eisenberg,E. and Levanon,E.Y. (2003) Preferential attachment in the protein network evolution. Phys. Rev. Lett., 91, 138701.
16. Faloutsos,M. et al. (1999) On power-law relationships of the Internet topology. Comp. Comm. R., 29, 251.
17. Forterre,P. and Philippe,H. (1999) Where is the root of the universal tree of life? Bioessays, 21, 871-879.
18. Freeman,L.C. (1977) A set of measures of centrality based on betweenness. Sociometry, 40, 35-41.
19. Friedman,R. and Hughes,A. (2002) Gene duplication and the structure of eukaryotic genomes. Genome Res., 11, 373-381.
20. Gu,Z. et al. (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol., 19, 256-262.
21. Hallinan,J. (2004) Gene duplication and hierarchical modularity in intracellular interaction networks. Biosystems, 74, 51-62.
22. Holland,P.W. (2003) More genes in vertebrates? J. Struct. Funct. Genomics, 3, 75-84.
23. Itzkovitz,S. et al. (2003) Subgraphs in random networks. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 68, 026127.
24. Jeong,H. et al. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
25. Kumar,S.R., Raghavan,P., Rajagopalan,S. and Tomkins,A. (1999) Trawling the Web for emerging cyber communities. Proceedings of the 8th WWW Conference, Amsterdam, The Netherlands, pp. 403-416.
26. Mangan,S. and Alon,U. (2003) Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA, 100, 11980-11985.
27. Milo,R. et al. (2002) Network motifs: Simple building blocks of complex networks. Science, 298, 824-827.
28. Newman,M.E. (2002) Assortative mixing in networks. Phys. Rev. Lett., 89, 208701.
29. Newman,M.E.J. (2001) The structure of scientific collaboration networks. Proc. Natl Acad. Sci. USA, 98, 404-409.
30. Pastor-Satorras,R. and Vespignani,A. (2001) Epidemic spreading in scale-free networks. Phys. Rev. Lett., 86, 3200-3203.
31. Ravasz,E. et al. (2002) Hierarchical organization of modularity in metabolic networks. Science, 297, 1551-1555.
32. Rzhetsky,A. and Gomez,S.M. (2001) Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics, 17, 988-996.
33. Seioghe,C. and Wolfe,K.H. (1999) Updated map of duplicated regions in the yeast genome. Gene, 238, 253-261.
34. Sidow,A. (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev., 6, 715-722.
35. Simon,H.A. (1955) On a class of skew distribution functions. Biometrica, 42, 425-440.
36. Sole,R and Pastor-Santorros,R. (2002) Complex networks in genomics and proteomics. Santa Fe Institute Working Paper.
37. Solomon,S. (1998) Stochastic Lotka-Volterra systems of competing auto-catalytic agents lead generically to truncated pareto power wealth distribution, truncated levy distribution of market returns, clustered volatility, booms and crashes. In Refenes,A.-P., Burgess,A.N. and Moody,J.E. (eds), Decision Technologies for Computational Finance. Kluwer Academic Publishers, The Netherlands.
38. Solomon,S. and Levy,M. (1996) Spontaneous scaling emergence in generic stochastic systems. Int. J. Mod. Phys. C., 7, 745.
39. Strogatz,S. (2001) Exploring random networks. Nature, 410, 268-276.
40. Stubbs,L. (2002) Genome comparison techniques. In Galas,D. and McCormack,S. (eds), Genomic Technologies:PResent and Future. Caister Academic Press, U.K.
41. Uetz,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
42. Venter,J.C. (2001) The sequence of the human genome. Science, 291, 1304-1351.
43. Wagner,A. (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol, 18, 1283-1292.
44. Watts,D.J. and Strogatz,S.H. (1998) Collective dynamics of 'small-world' networks. Nature, 393, 440-442.
45. Wolfe,K.H. and Shields,D.C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387, 708-713.
46. Wu,F. et al. (2004) Information flow in social groups. Phys. Stat. Mech. Appl., 337, 327-335.