The effects of incomplete protein interaction data on structural and evolutionary inferences

BMC Biology

Volumn 4, Issue , 2006, Pages

  de Silva, Eric ^a   Thorne, Thomas ^a   Ingram, Piers ^a,b   Agrafioti, Ino ^a   Swire, Jonathan ^a   Wiuf, Carsten ^c,d   Stumpf, Michael P H ^a,b  

^a Centre for Bioinformatics   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c AARHUS UNIVERSITY   (Denmark)

^d AARHUS UNIVERSITY HOSPITAL   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BIOINFORMATICS; BIOSTATISTICS; DATA ANALYSIS; INFERENTIAL STATISTICS; MOLECULAR EVOLUTION; NONHUMAN; PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SAMPLING; STRUCTURAL PROTEOMICS; SYSTEMS BIOLOGY; BIOLOGICAL MODEL; GENE REGULATORY NETWORK; GENETICS; PROTEIN ANALYSIS;

EVOLUTION, MOLECULAR; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 33845262280     PISSN: 17417007     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-4-39     Document Type: Article

References (45)

1. de Silva E, Stumpf M: Complex networks and simple models in biology. J Roy Soc Interface 2005, 2(5):419-30.
2. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck F, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker E: A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122(6):957-68.
3. Rual J, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz G, Gibbons F, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg D, Zhang L, Wong S, Franklin G, Li S, Albala J, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski R, Vandenhaute J, Zoghbi H, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick M, Hill D, Roth F, Vidal M: Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437(7062):1173-8.
4. Stumpf M, Wiuf C, May R: Subnets of scale-free networks are not scale-free: the sampling properties of networks. Proc Natl Acad Sci USA 2005, 102:4221-4224.
5. Stumpf M, Wiuf C: Sampling properties of random graphs: the degree distribution. Phys Rev E 2005, 72:036118.
6. Han J, Dupuy D, Bertin N, Cusick M, Vidal M: Effect of sampling on topology predictions of protein-protein interaction networks. Nature Biotechnol 2005, 23:839-844.
7. Lee S, Kim P, Jeong H: Statistical properties of sampled networks. Phys Rev E 2006, 73:016102.
8. Hakes L, Robertson D, Oliver S: Effect of dataset selection on the topological interpretation of protein interaction networks. BMC Genomics 2005, 6:131.
9. Evans T: Complex Networks. Contemporary Physics 2004, 45(6):455-474.
10. Wiuf C, Stumpf M: Binomial sampling. Proc Royal Soc A 2006, 462:1181-1195.
11. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: Simple building blocks of complex networks. Science 2002, 298(5594):824-827.
12. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U: Superfamilies of evolved and designed networks. Science 2004, 303(5663):1538-1542.
13. Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 2004, 22:78-85.
14. Lappe M, Holm L: Unraveling protein interaction networks with near-optimal efficiency. Nat Biotechnol 2004, 22:98-103.
15. Berg J, Lässig M: Correlated random networks. Phys Rev Lett 2002, 89:228701.
16. Burda Z, Krzywicki A: Uncorrelated Random Networks. Phys Rev E 2004, 67:046118.
17. Cox D, Hinkley D: Theoretical Statistics New York. Chapman&Hall/CRC; 1974.
18. Bollobás B: Random Graphs Academic Press; 1998.
19. Newman M, Strogatz S, Watts D: Random graphs with arbitrary degree distributions and their applications. Phys Rev E 2001, 64:026118.
20. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data of protein-protein interactions. Nature 2002, 417(6887):399-403.
21. Ebel H, Mielsch L, Bornholdt S: Scale-free topology of e-mail networks. Phys Rev E 2002, 66(035103):.
22. Agrafioti I, Swire J, Abbott I, Huntley D, Butcher S, Stumpf M: Comparative analysis of the Saccaromyces cerevisiae and Caenorhabditis elegans protein interaction networks. BMC Evolutionary Biology 2005, 5:23.
23. Nye T, Berzuini C, Gilks W, Babu M, Teichmann S: Statistical analysis of domains in interacting protein pairs. Bioinformatics 2005, 21:993-1001.
24. Database of Interacting Proteins (DIP) [http://dip.doe-mbi.ucla.edu]
25. Wuchty S, Oltvai Z, Barabsi AL: Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 2003, 35(2):176-9.
26. Mazurie A, Bottani S, Vergassola M: An evolutionary and functional assessment of regulatory network motifs. Genome Biology 2005, 6:R35.
27. Ingram P, Stumpf M, Stark J: Network motifs: structure does not determine function. BMC Genomics 2006, 7:108.
28. Gavin M, Bosche M, Krause R, Grandi P, Marzioch M, Schultz J, Rick J, Michon A, Cruciat C, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Hudak M, Dickson D, Rudi T, Ganu V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier M, Copley R, Edelmann A, Querfurth E, V R, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, G SF: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
29. Yook SH, Oltvai ZN, Barabsi AL: Functional and topological characterization of protein interaction networks. Proteomics 2004, 4(4):928-42.
30. Stumpf M, Ingram P: Probability models for degree distributions of protein interaction networks. Europhys Lett 2005, 71:152-158.
31. Newman M: The structure and function of complex networks. SIAM Review 2003, 45(2):167-256.
32. Kashtan N, Itzkovitz: S, Milo R, Alon U: Topological generalizations of network motifs. Physical Review E 2004, 70(3):. art. no.031909.
33. Maslov S, Sneppen K, Alon U: Correlation profiles and motifs in complex networks. In Handbook of Graphs and Networks Wiley-VCH; 2003.
34. Kashtan N, Itzkovitz S, Milo R, Alon U: Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004, 20(11):1746-1758.
35. Kuramochi M, Karypis G: An efficient algorithm for discovering frequent subgraphs. IEEE Transactions in Knowledge Discovery and Engineering 2002.
36. Luscombe N, Babu M, Yu H, Snyder M, Teichmann S, Gerstein M: Genomic analysis of regulatory network dynamics reveals large topological change. Nature 2004, 431:308-312.
37. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW: Evolutionary rate in the protein interaction network. Science 2002, 296(5568):750-2.
38. Ewens W: Mathematical Population Genetics 2nd edition. New York: Springer, 2004.
39. Tong AHY, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Mnard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C: Global mapping of the yeast genetic interaction network. Science 2004, 303(5659):808-13.
40. Cho R, Campbell M, Winzeler E, Steinmetz L, Conway A, Wodicka L, Wolfsberg T, Gabrielian A, Landsman D, Lockhart D, Davies R: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998, 2:65-73.
41. Dorogovtsev S, Mendes J: Evolution of Networks Oxford University Press; 2003.
42. Watts D, Strogatz: S: Collective dynamics of small-world networks. Nature 1998, 393:440-442.
43. Goh KI, Oh E, Jeong H, Kahng B, Kim D: Classification of scale-free networks. Proc Natl Acad Sci USA 2002, 99(20):12583-8.
44. Ewens W, Grant G: Statistical Methods in Bioinformatics New York: Springer; 2001.
45. Wuchty S, Stadler PF: Centers of complex networks. J Theor Biol 2003, 223:45-53.