Effect of sampling on topology predictions of protein-protein interaction networks

Nature Biotechnology

Volumn 23, Issue 7, 2005, Pages 839-844

  Han, Jing Dong J ^a,b,c   Dupuy, Denis ^a,b   Bertin, Nicolas ^a,b   Cusick, Michael E ^a,b   Vidal, Marc ^a,b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; EXTRAPOLATION; SAMPLING; YEAST;

PROTEIN-PROTEIN INTERACTION (PPI); SCALE-FREE TOPOLOGIES; YEAST TWO-HYBRID (Y2H);

PROTEINS;

COMPUTER MODEL; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN PROTEIN INTERACTION; REVIEW; SAMPLING; SIMULATION; YEAST; ANIMAL; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PROTEOMICS; TWO HYBRID SYSTEM;

PROTEIN;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 24944442468     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1116     Document Type: Review

References (51)

1. Barabási, A.L. & Oltvai, Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
2. Strogatz, S.H. Exploring complex networks. Nature 410, 268-276 (2001).
3. Barabási, A.L., Albert, R. & Jeong, H. Scale-free characteristics of random networks: the topology of the world-wide web. Physics A (Amsterdam) 281, 69-77 (2000).
4. Yook, S.H., Jeong, H. & Barabasi, A.L. Modeling the Internet's large-scale topology. Proc. Natl. Acad. Sci. USA 99, 13382-13386 (2002).
5. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
6. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569-4574 (2001).
7. Reboul, J. et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34, 35-41 (2003).
8. Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736 (2003).
9. Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004).
10. Han, J.D. et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88-93 (2004).
11. Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
12. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
13. Walhout, A.J., Boulton, S.J. & Vidal, M. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17, 88-94 (2000).
14. Edwards, A.M. et al. Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet. 18, 529-536 (2002).
15. Bader, G.D. & Hogue, C.W. Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20, 991-997 (2002).
16. von Mering, C. et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403 (2002).
17. Grigoriev, A. On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res. 31, 4157-4161 (2003).
18. Ito, T. et al. Roles for the two-hybrid system in exploration of the yeast protein interactome. Mol. Cell. Proteomics 1, 561-566 (2002).
19. Formstecher, E. et al. Protein interaction mapping: A Drosophila case study. Genome Res. 15, 376-384 (2005).
20. Stumpf, M.P., Wiuf, C. & May, R.M. Subnets of scale-free networks are not scale-free: Sampling properties of networks. Proc. Natl. Acad. Sci. USA (2005).
21. Przulj, N., Corneil, D.G. & Jurisica, I. Modeling interactome: scale-free or geometric? Bioinformatics 20, 3508-3515 (2004).
22. Jeong, H., Mason, S.P., Barabasi, A.L. & Oltvai, Z.N. Lethality and centrality in protein networks. Nature 411, 41-42 (2001).
23. Thomas, A., Cannings, R., Monk, N.A. & Cannings, C. On the structure of protein-protein interaction networks. Biochem. Soc. Trans. 31, 1491-1496 (2003).
24. Yook, S.H., Oltvai, Z.N. & Barabasi, A.L. Functional and topological characterization of protein interaction networks. Proteomics 4, 928-942 (2004).
25. Erdös, P. & Rényi, A. On the evolution of random graphs. Publ. Math. Inst. Hung. Acad. Sci. 5, 17-60 (1960).
26. Barabási, A.L. & Albert, R. Emergence of scaling in random networks. Science 286, 509-512 (1999).
27. Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563-547 (1996).
28. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018 (1998).
29. Adams, M.D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
30. Schwikowski, B., Uetz, P. & Fields, S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18, 1257-1261 (2000).
31. Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 293, 2101-2105 (2001).
32. Tong, A. H. et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295, 321-324 (2002).
33. Walhout, A.J. & Vidal, M. A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome Res. 9, 1128-1134 (1999).
34. Legrain, P., Wojcik, J. & Gauthier, J.M. Protein-protein interaction maps: a lead towards cellular functions. Trends Genet. 17, 346-352 (2001).
35. Vidalain, P.O., Boxem, M., Ge, H., Li, S. & Vidal, M. Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 32, 363-370 (2004).
36. Albert, R., Jeong, H. & Barabasi, A.L. Error and attack tolerance of complex networks. Nature 406, 378-382 (2000).
37. Wagner, A. Robustness against mutations in genetic networks of yeast. Nat. Genet. 24, 355-361 (2000).
38. Vogelstein, B., Lane, D. & Levine, A.J. Surfing the p53 network. Nature 408, 307-310 (2000).
39. Apic, G., Ignjatovic, T., Boyer, S. & Russell, R.B. Illuminating drug discovery with biological pathways. FEBS Lett. 579, 1872-1877 (2005).
40. Lappe, M. & Holm, L. Unraveling protein interaction networks with near-optimal efficiency. Nat. Biotechnol. 22, 98-103 (2004).
41. Eisenberg, E. & Levanon, E.Y. Preferential attachment in the protein network evolution. Phys. Rev. Lett. 91, 138701 (2003).
42. Qin, H., Lu, H.H., Wu, W.B. & Li, W.H. Evolution of the yeast protein interaction network. Proc. Natl. Acad. Sci. USA 100, 12820-12824 (2003).
43. Pereira-Leal, J.B., Audit, B., Peregrin-Alvarez, J.M. & Ouzounis, C.A. An exponential core in the heart of the yeast protein interaction network. Mol. Biol. Evol. 22, 421-425 (2004).
44. Hartwell, L.H., Hopfield, J.J., Leibler, S. & Murray, A.W. From molecular to modular cell biology. Nature 402, C47-C52 (1999).
45. Poyatos, J.F. & Hurst, L.D. How biologically relevant are interaction-based modules in protein networks? Genome Biol. 5, R93 (2004).
46. Bork, P. et al. Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14, 292-299 (2004).
47. Dunn, R., Dudbridge, F. & Sanderson, C.M. The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 6, 39 (2005).
48. Shen-Orr, S.S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68 (2002).
49. Rives, A.W. & Galitski, T. Modular organization of cellular networks. Proc. Natl. Acad. Sci. USA 100, 1128-1133 (2003).
50. Bader, G.D. & Hogue, C.W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2 (2003).
51. Pereira-Leal, J.B., Enright, A.J. & Ouzounis, C.A. Detection of functional modules from protein interaction networks. Proteins 54, 49-57 (2004).