Evolution at the system level: the natural history of protein interaction networks

Trends in Ecology and Evolution

Volumn 22, Issue 7, 2007, Pages 366-373

  Stumpf, Michael P H ^a   Kelly, William P ^a   Thorne, Thomas ^a   Wiuf, Carsten ^b  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY BIOLOGY; METHODOLOGY; MOLECULAR ANALYSIS; PHENOTYPE; PHYLOGENETICS; PROTEIN;

ANIMAL; BIOLOGICAL MODEL; EVOLUTION; PROTEIN ANALYSIS; REVIEW;

ANIMALS; EVOLUTION; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING;

EID: 34250322596     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2007.04.004     Document Type: Review

References (83)

1. Burda Z., et al. Statistical ensemble of scale-free random graphs. Phys. Rev. E 64 (2001) 046118
2. Evans T. Complex networks. Contemp. Phys. 45 (2004) 455-474
3. Scott J. Social Network Analysis: A Handbook (2000), Sage Publications
4. Wagner A. How the global structure of protein interaction networks evolves. Proc. Biol. Sci. 270 (2003) 457-466
5. Alm E., and Arkin A.P. Biological networks. Curr. Opin. Struct. Biol. 13 (2003) 193-202
6. de Silva, E. and Stumpf, M. Complex networks and simple models in biology. J. R. Soc. Interface (in press)
7. Bollobás B. Random Graphs (1998), Academic Press
8. Newman M. The structure and function of complex networks. SIAM Rev. 45 (2003) 167-256
9. Dorogovtsev S., and Mendes J. Evolution of Networks (2003), Oxford University Press
10. Sugihara G. Graph theory, homology and food webs. Proc. Symp. Appli. Math. 30 (1984) 83-101
11. Proulx S.R., et al. Network thinking in ecology and evolution. Trends Ecol. Evol. 20 (2005) 345-353
12. May R.M. Network structure and the biology of populations. Trends Ecol. Evol. 21 (2006) 394-399
13. Bürger R. The Mathematical Theory of Selection, Recombination, and Mutation (2000), John Wiley & Sons
14. Ewens W. Mathematical Population Genetics. 2nd edn (2004), Springer
15. Haldane J.B. A defense of beanbag genetics. Perspect. Biol. Med. 19 (1964) 343-359
16. Kacser H., and Burns J. The control of flux. Symp. Soc. Exp. Biol. 27 (1973) 65-104
17. Kacser H., and Burns J. Molecular democracy: who shares the controls. Biochem. Soc. Trans. 7 (1979) 1149-1160
18. Keightley P.D. Models of quantitative variation of flux in metabolic pathways. Genetics 121 (1989) 869-876
19. Frank S.A. Population and quantitative genetics of regulatory networks. J. Theor. Biol. 197 (1999) 281-294
20. Kauffman S. The Origins of Order (1993), Oxford University Press
21. Dorogovtsev S.N., et al. Structure of growing networks with preferential linking. Phys. Rev. Lett. 85 (2000) 4633-4636
22. Chung F., et al. Duplication models for biological networks. J. Comput. Biol. 10 (2003) 677-687
23. Barabasi A.L., and Albert R. Emergence of scaling in random networks. Science 286 (1999) 509-512
24. Thomas A., et al. On the structure of protein-protein interaction networks. Biochem. Soc. Trans. 31 (2003) 1491-1496
25. Stumpf M., and Ingram P. Probability models for degree distributions of protein interaction networks. Europhys. Lett. 71 (2005) 152-158
26. Stumpf M., et al. Statistical model selection methods applied to biological networks. Trans. Comput. Systems Biol. 3 (2005) 65-72
27. Tanaka R., et al. Some protein interaction data do not exhibit power law statistics. FEBS Lett. 579 (2005) 5140-5144
28. Khanin R., and Wit E. How scale-free are biological networks?. J. Comput. Biol. 13 (2006) 810-818
29. Dorogovtsev S.N., et al. Multifractal properties of growing networks. Europhys. Lett. 57 (2002) 334-338
30. Wiuf C., et al. A likelihood approach to the analysis of network data. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 7566-7570
31. Berg J., et al. Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol. Biol. 5 (2004) 51
32. Durbin R., et al. Biological Sequence Analysis (1998), Cambridge University Press
33. Koshi J.M., and Goldstein R.A. Models of natural mutations including site heterogeneity. Proteins 32 (1998) 289-295
34. von Mering C., et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417 (2002) 399-403
35. Bader J.S., et al. Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 22 (2004) 78-85
36. Stumpf M.P., et al. Subnets of scale-free networks are not scale-free: the sampling properties of networks. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 4221-4224
37. Stumpf M.P., and Wiuf C. Sampling properties of random graphs: the degree distribution. Phys. Rev. E 72 (2005) 036118
38. Han J.D., et al. Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol. 23 (2005) 839-844
39. de Silva E., et al. The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biol. 4 (2006) 39
40. Hakes L., et al. Effect of dataset selection on the topological interpretation of protein interaction networks. BMC Genom. 6 (2005) 131
41. Reguly T., et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol. 5 (2006) 11
42. Fraser H.B., et al. Evolutionary rate in the protein interaction network. Science 296 (2002) 750-752
43. Fraser H.B., et al. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol. Biol. 3 (2003) 11
44. Wuchty S., et al. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 35 (2003) 176-179
45. Wuchty S. Evolution and topology in the yeast protein interaction network. Genome Res. 14 (2004) 1310-1314
46. Bloom J., and Adami C. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol. Biol. 3 (2003) 21
47. Jordan I.K., et al. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3 (2003) 1
48. Kunin V., et al. Functional evolution of the yeast protein interaction network. Mol. Biol. Evol. 21 (2004) 1171-1176
49. Agrafioti I., et al. Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. BMC Evol. Biol. 5 (2005) 23
50. Drummond D.A., et al. A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23 (2006) 327-337
51. Salathé M., et al. The effect of multifunctionality on the rate of evolution in yeast. Mol. Biol. Evol. 23 (2006) 721-722
52. Manke T., et al. Correlating protein-DNA and protein-protein interaction networks. J. Mol. Biol. 333 (2003) 75-85
53. Lemos B., et al. Regulatory evolution across the protein interaction network. Nat. Genet. 36 (2004) 1059-1060
54. Makino T., and Gojobori T. The evolutionary rate of a protein in influenced by features of the interacting partners. Mol. Biol. Evol. 23 (2006) 784-789
55. Deng M., et al. Mapping gene ontology to proteins based on protein-protein interaction data. Bioinformatics 20 (2004) 895-902
56. Rives A.W., and Galitski T. Modular organization of cellular networks. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 1128-1133
57. Gagneur J., et al. Modular decomposition of protein-protein interaction networks. Genome Biol. 5 (2004) R57
58. Han J.D., et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430 (2004) 88-93
59. Yook S.-H., et al. Functional and topological characterization of protein interaction networks. Proteomics 4 (2004) 928-942
60. Milo R., et al. Network motifs: Simple building blocks of complex networks. Science 298 (2002) 824-827
61. Milo R., et al. Superfamilies of evolved and designed networks. Science 303 (2004) 1538-1542
62. Kuramochi M., and Karypis G. An efficient algorithm for discovering frequent subgraphs. IEEE Trans. Know. Disc. Eng. 16 (2004) 1038-1051
63. Girvan M., and Newman M. Community structure in social and biological networks. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 7821-7826
64. Ingram P., et al. Network motifs: structure does not determine function. BMC Genomics 7 (2006) 108
65. Kollmann M., et al. Design principles of a bacterial signalling network. Nature 438 (2005) 504-507
66. Chothia C., et al. Evolution of the protein repertoire. Science 300 (2003) 1701-1703
67. Orengo C.A., and Thornton J.M. Protein families and their evolution-a structural perspective. Annu. Rev. Biochem. 74 (2005) 867-900
68. Deng M., et al. Inferring domain-domain interactions from protein-protein interactions. Genome Res. 12 (2002) 1540-1548
69. Aloy P., et al. Structure-based assembly of protein complexes in yeast. Science 303 (2004) 2026-2029
70. Berg J., and Lässig M. Local graph alignment and motif search in biological networks. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 14689-14694
71. Kelley B.P., et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 11394-11399
72. Sharan R., et al. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 1974-1979
73. Koyutürk M., et al. Pairwise alignment of protein interaction networks. J. Comput. Biol. 13 (2006) 182-199
74. Berg J., and Lässig M. Cross species analysis of biological networks by Bayesian alignment. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 10967-10972
75. Suthram S., et al. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438 (2005) 108-112
76. Gilles C., et al. Crystallization and preliminary x-ray analysis of pig porcine pancreatic alpha-amylase in complex with a bean lectin-like inhibitor. Acta Crystallogr. D 52 (1996) 581-582
77. Callaway D.S., et al. Network robustness and fragility: Percolation on random graphs. Phys. Rev. Lett. 85 (2000) 5468-5471
78. Uetz P., et al. A comprehensive analysis of protein-protein interaction networks in Saccharomyces cerevisiae. Nature 403 (2000) 623-627
79. Ito T., et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 4569-4574
80. Fraser H.B., and Hirsh A.E. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol. Biol. 4 (2004) 13
81. Xenarios I., et al. Dip: the database of interacting proteins. Nucleic Acids Res. 28 (2000) 289-291
82. Mewes H.W., et al. Mips: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 34 Suppl. 1 (2005) D169-D172
83. Giot L., et al. A protein interaction map of Drosophila melanogaster. Science 302 (2003) 1727-1736