A direct comparison of protein interaction confidence assignment schemes

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Suthram, Silpa ^a,b   Shlomi, Tomer ^c   Ruppin, Eytan ^c   Sharan, Roded ^c   Ideker, Trey ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

FALSE POSITIVE DETECTION; HIGH-THROUGHPUT MEASUREMENTS; PERFORMANCE ASSESSMENT; PROBABILITY ASSIGNMENT; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS; SEQUENCE CONSERVATION; TECHNOLOGICAL ADVANCES;

COMPLEX NETWORKS; CONSERVATION;

PROTEINS;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONSERVATION GENETICS; CONTROLLED STUDY; CORRELATION ANALYSIS; FUNCTIONAL PROTEOMICS; GENETIC SIMILARITY; INTERMETHOD COMPARISON; METHODOLOGY; NONHUMAN; PROBABILITY; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIGNAL NOISE RATIO; YEAST; COMPARATIVE STUDY; GENETICS; METABOLISM; PROCEDURES; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; REPRODUCIBILITY; SEQUENCE ALIGNMENT;

CAENORHABDITIS ELEGANS PROTEIN; DROSOPHILA PROTEIN; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEIN;

CAENORHABDITIS ELEGANS PROTEINS; DATABASES, PROTEIN; DROSOPHILA PROTEINS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 33747586075     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-360     Document Type: Article

References (39)

1. Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature 1989, 340:245-246.
2. 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, 415:141-147.
3. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutiller 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, 415:180-183.
4. 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 USA 2001, 98:4569-4574.
5. 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, 403:623-627.
6. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL Jr, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM: A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736.
7. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M: A map of the interactome network of the metazoan C. elegans. Science 2004, 303:540-543.
8. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE: A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122:957-968.
9. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M: Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437:1173-1178.
10. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
11. Grigoriev A: A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2001, 29:3513-3519.
12. 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, 1:349-356.
13. Deng M, Sun F, Chen T: Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput 2003:140-151.
14. Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 2004, 22:78-85.
15. Goldberg DS, Roth FP: Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA 2003, 100:4372-4376.
16. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D: A combined algorithm for genome-wide prediction of protein function. Nature 1999, 402:83-86.
17. von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P: STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 2005, 33:D433-437.
18. Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG: Discovery of biological networks from diverse functional genomic data. Genome Biol 2005, 6:R114.
19. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302:449-453.
20. Qi Y, Klein-Seetharaman J, Bar-Joseph Z: Random forest similarity for protein-protein interaction prediction from multiple sources. Pac Symp Biocomput 2005:531-542.
21. Qi Y, Bar-Joseph Z, Klein-Seetharaman J: Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 2006, 63:490-500.
22. Suthram S, Sittler T, Ideker T: The Plasmodium protein network diverges from those of other eukaryotes. Nature 2005, 438:108-112.
23. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T: Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 2005, 102:1974-1979.
24. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
25. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305.
26. Mewes HW, Albermann K, Heumann K, Liebl S, Pfeiffer F: MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res 1997, 25:28-30.
27. Supplementary Website [http://chianti.ucsd.edu/Suthram2006]
28. Pagel P, Mewes HW, Frishma D: Conservation of protein-protein interactions - lessons from ascomycota. Trends Genet 2004, 20:72-76.
29. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M: Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 2004, 14:1107-1118.
30. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
31. Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G: The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res 2005, 33:D580-582.
32. Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2.
33. Hu H, Yan X, Huang Y, Han J, Zhou XJ: Mining coherent dense subgraphs across massive biological networks for functional discovery. Bioinformatics 2005, 21 (Suppl 1):i213-i221.
34. Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T: Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci USA 2003, 100:11394-11399.
35. Spirin V, Mirny LA: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003, 100:12123-12128.
36. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW: Evolutionary rate in the protein interaction network. Science 2002, 296:750-752.
37. Weston JSM, Chapelle O, Pontil M, Poggio T, Vapnik V: Feature selection for SVMs. Avd In Neural Inf Proc Syst 13 2001.
38. Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM: Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res 2004, 32:D311-314.
39. Shanmugan KS: Digital and analog communication systems New York: Wiley; 1979.