A unified representation of multiprotein complex data for modeling interaction networks

Proteins: Structure, Function and Genetics

Volumn 57, Issue 1, 2004, Pages 99-108

  Ding, Chris ^a   He, Xiaofeng ^a   Meraz, Richard F ^a   Holbrook, Stephen R ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Bipartite graphic; Cluster analysis; Gene ontology; Network biology; Protein complex; Supercomplex

Indexed keywords

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPLEX FORMATION; DATA ANALYSIS; HIGH THROUGHPUT SCREENING; MACROMOLECULE; MASS SPECTROMETRY; MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION;

ALGORITHMS; MODELS, CHEMICAL; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, QUATERNARY; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE;

EID: 4444260148     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20147     Document Type: Article

References (35)

1. 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.
2. 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.
3. 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;415:180-183.
4. 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.
5. Alm E, Arkin AP. Biological networks. Curr Opin Struct Biol 2003;13:193-202.
6. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000;18:1257-1261.
7. Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003;4:2.
8. Pothen A. Graph and hypergraph models of protein interaction networks. SIAM Conf Comput Sci Eng 2003.
9. Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res 2003;31:2443-2450.
10. Krause R, Von Mering C, Bork P. A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. Bioinformatics 2003;19:1901-1908.
11. Deshaies RJ, Seol JH, McDonald WH, Cope G, Lyapina S, Shevchenko A, Verma R, Yates JR III. Charting the protein complexome in yeast by mass spectrometry. Mol Cell Proteomics 2002;1:3-10.
12. Ding C. Analysis of gene expression profiles: class discovery and leaf node ordering. Proc 6th Intl Conf Comp Mol Bio (RECOMB) 2002;6:127-136.
13. Ding C, He X, Zha H, Gu M, Simon H. A min-max cut algorithm for graph partitioning and data clustering. Proc IEEE Intl Conf Data Mining (ICDM) 2001:107-114.
14. Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 2002;30:69-72.
15. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000;16:276-277.
16. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
17. Deng M, Sun F, Chen T. Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput 2003:140-151.
18. 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.
19. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary rate in the protein interaction network. Science 2002;296:750-752.
20. Bader GD, Hogue CW. Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 2002;20:991-997.
21. Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003;100:12123-12128.
22. Vazquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 2003;21:697-700.
23. Nooren IM, Thornton JM. Diversity of protein-protein interactions. EMBO J 2003;22:3486-3492.
24. Veselovsky AV, Ivanov YD, Ivanov AS, Archakov AI, Lewi P, Janssen P. Protein-protein interactions: mechanisms and modification by drugs. J Mol Recognit 2002;15:405-422.
25. Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
26. Gavin AC, Superti-Furga G. Protein complexes and proteome organization from yeast to man. Curr Opin Chem Biol 2003;7:21-27.
27. 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.
28. Maniatis T, Reed R. An extensive network of coupling among gene expression machines. Nature 2002;416:499-506.
29. Graack HR, Wittmann-Liebold B. Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J 1998;329:433-448.
30. Reed R, Hurt E. A conserved mRNA export machinery coupled to pre-mRNA splicing. Cell 2002;108:523-531.
31. Keene JD. Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 2001;98:7018-7024.
32. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B. MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002;30:31-34.
33. Roth SY, Denu JM, Allis CD. Histone acetyltransferases. Annu Rev Biochem 2001;70:81-120.
34. Green CM, Almouzni G. When repair meets chromatin. First in series on chromatin dynamics. EMBO Rep 2002;3:28-33.
35. Peterson CL. Chromatin remodeling enzymes: taming the machines. Third in review series on chromatin dynamics. EMBO Rep 2002;3:319-322.