Effect of dataset selection on the topological interpretation of protein interaction networks

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Hakes, Luke ^a   Robertson, David L ^a   Oliver, Stephen G ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE PROTEIN; FUNGAL PROTEIN;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; HIGH THROUGHPUT SCREENING; MATHEMATICAL COMPUTING; METHODOLOGY; NONHUMAN; PROTEIN DATABASE; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; RANDOMIZATION; SACCHAROMYCES CEREVISIAE; THEORETICAL STUDY; BIOLOGICAL MODEL; BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; FUNGAL GENE; GENETIC DATABASE; GENETIC SELECTION; GENETICS; GENOMICS; METABOLISM; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEOMICS; THEORETICAL MODEL;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; FUNGAL PROTEINS; GENES, FUNGAL; GENOMICS; MODELS, GENETIC; MODELS, THEORETICAL; PROGRAMMING LANGUAGES; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEOMICS; RANDOM ALLOCATION; SACCHAROMYCES CEREVISIAE; SELECTION, GENETIC; SOFTWARE;

EID: 26444506831     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-131     Document Type: Article

References (24)

1. Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E: Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO Rep 2004, 5(3):274-279.
2. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL: The large-scale organization of metabolic networks. Nature 2000, 407(6804):651-654.
3. Ma H, Zeng AP: Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19(2):270-277.
4. Wagner A, Fell DA: The small world inside large metabolic networks. Proc R Soc Lond B Biol Sci 2001, 268(1478):1803-1810.
5. Wuchty S: Evolution and topology in the yeast protein interaction network. Genome Res 2004, 14(7):1310-1314.
6. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415(6868):141-147.
7. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415(6868):180-183.
8. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 2001, 98(8):4569-4574.
9. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-627.
10. Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42.
11. Wagner A: The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 2001, 18(7):1283-1292.
12. Wuchty S: Interaction and domain networks of yeast. Proteomics 2002, 2(12):1715-1723.
13. Albert R, Jeong H, Barabasi AL: Error and attack tolerance of complex networks. Nature 2000, 406(6794):378-382.
14. Maslov S, Sneppen K: Specificity and stability in topology of protein networks. Science 2002, 296(5569):910-913.
15. Pereira-Leal JB, Audit B, Peregrin-Alvarez JM, Ouzounis CA: An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol 2005, 22(3):421-425.
16. Bader GD, Hogue CW: Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 2002, 20(10):991-997.
17. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, 32(Database issue):D449-451.
18. Deane CM, Salwinski L, Xenarios I, Eisenberg D: Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 2002, 1(5):349-356.
19. Cornell M, Paton NW, Oliver SG: A critical and integrated view of the yeast interactome. Comparative and Functional Genomics 2004(5):382-402.
20. Vidalain PO, Boxem M, Ge H, Li S, Vidal M: Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 2004, 32(4):363-370.
21. Tong AH, 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, Menard 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):808-813.
22. Barabasi AL, Albert R: Emergence of scaling in random networks. Science 1999, 286(5439):509-512.
23. Spirin V, Mirny LA: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 2003, 100(21):12123-12128.
24. Saccharomyces Gene Deletion Project http://www-sequence.stanford.edu/group/yeast_deletion_project/ Essential_ORFs.txt