Topological structure analysis of the protein-protein interaction network in budding yeast

Nucleic Acids Research

Volumn 31, Issue 9, 2003, Pages 2443-2450

  Bu, Dongbo ^a   Zhao, Yi ^a   Cai, Lun ^a   Xue, Hong ^b   Zhu, Xiaopeng ^b   Lu, Hongchao ^a   Zhang, Jingfen ^a   Sun, Shiwei ^a   Ling, Lunjiang ^b   Zhang, Nan ^b   Li, Guojie ^a   Chen, Runsheng ^a,b  

^a INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^b INSTITUTE OF BIOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; BUDDING; CLASSIFICATION; CONTROLLED STUDY; DATA ANALYSIS; MOLECULAR BIOLOGY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SPECTROSCOPY; STRUCTURE ANALYSIS; THEORY; YEAST; ALGORITHM; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; METABOLISM; PROTEIN BINDING; SACCHAROMYCES;

SACCHAROMYCETALES;

PROTEIN;

ALGORITHMS; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEINS; SACCHAROMYCETALES;

EID: 0038074373     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg340     Document Type: Article

References (33)

1. Fields,S. (1997) The future is function. Nature Genet., 15, 325-327.
2. Rain,J.C., Selig,L., De Reuse,H., Battaglia,V., Reverdy,C., Simon,S., Lenzen,G., Petel,F., Wojcik,J., Schachter,V., Chemama,Y., Labigne,A. and Legrain,P. (2001) The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-215.
3. Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A., Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
4. von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
5. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Narayan,V., Lockshon,D., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
6. Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
7. Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., Millar,A., Taylor,P., Bennett,K., Boutilier,K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
8. Cho,R.J., Campbell,M.J., Winzeler,E.A., Steinmetz,L. Conway,A., Wodicka,L., Wolfsberg,T.G., Gabrielian,A.E., Landsman,D., Lockhart,D.J. and Davis,R.W. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
9. Hughes,T.R., Marton,M.J., Jones,A.R., Roberts,C.J., Stoughton,R., Armour,C.D., Bennett,H.A., Coffey,E., Dai,H., He,Y.D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
10. Tong,A.H., Drees,B., Nardelli,G., Bader,G.D., Brannetti,B., Castagnoli,L., Evangelista,M., Ferracuti,S., Nelson,B., Paoluzi,S. et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science, 294, 2364-2368.
11. Mewes,H.W., Frishman,D., Gildener,U., Mannhaupt,G., Mayer,K., Mokrejs,M., Morgenstern,B., Munsterkotter,M. et al. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res., 30, 31-34.
12. Enright,A.J., Iliopoulos,I., Kyrpides,N.C. and Ouzounis,C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
13. Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
14. Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
15. Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
16. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
17. Huynen,M.A. and Bork,P. (1998) Measuring genome evolution. Proc. Natl Acad. Sci. USA, 95, 5849-5856.
18. Schwikowski,B., Uetz,P. and Fields,S. (2000) A network of protein-protein interactions in yeast. Nat. Biotechnol., 18, 1257-1261.
19. Hishigaki,H., Nakai,K., Ono,T., Tanigami,A. and Takagi,T. (2001) Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast, 18, 523-531.
20. Maslov,S. and Sneppen,K. (2002) Specificity and stability in topology of protein networks. Science, 296, 910-913.
21. Ge,H., Liu,Z., Church,G.M. and Vidal,M. (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genet., 29, 482-486.
22. Fraser,H.B., Hirsh,A.E., Steinmetz,L.M., Scharfe,C. and Feldman,M.W. (2002) Evolutionary rate in the protein interaction network. Science, 296, 750-752.
23. Gibson,D., Kleinberg,J. and Raghavan,P. (1998) Inferring Web communities from link topology. Proceedings of the 9th ACM Conference on Hypertext and Hypermedia. ACM Press, New York, NY.
24. Kleinberg,J. (1998) Authoritative sources in a hyper-linked environment. Proceedings of the 9th ACM Conference on Hypertext and Hypermedia. ACM Press, New York, NY.
25. Bollobas,B. (1998) Modern Graph Theory. Springer-Verlag, Inc., New York, NY, pp. 3-77.
26. Watts,D.J. and Strogatz,S.H. (1998) Collective dynamics of 'small-world' networks. Nature, 393, 440-442.
27. Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architecture. Nature Genet., 22, 281-285.
28. Wu,L.F., Hughes,T.R., Davierwala,A.P., Robinson,M.D., Stoughton,R. and Altschuler,S.J. (2002) Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genet., 31, 255-265.
29. Harnpicharnchai,P., Jakovljevic,J., Horsey,E., Miles,T., Roman,J., Rout,M., Meagher,D., Imai,B., Guo,Y., Brame,C.J. et al. (2001) Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol. Cell, 8, 505-515.
30. Bassler,J., Grandi,P., Gadal,O., Lessmann,T., Petfalski,E., Tollervey,D., Lechner,J. and Hurt,E. (2001) Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol. Cell, 8, 517-529.
31. Dragon,F., Gallagher,J.E., Compagnone-Post,P.A., Mitchell,B.M., Porwancher,K.A., Wehner,K.A., Wormsley,S., Settlage,R.E., Shabanowitz,J., Osheim,Y. et al. (2002) A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature, 417, 967-970.
32. Alberts,B., Bray,D., Lewis,J., Raff,M., Roberts,K. and Watson,D.J. (1994) Molecular Biology of the Cell, 3rd Edn. Garland, New York, NY.
33. Lodish,H., Berk,A., Zipursky,S.L., Matsudaira,P., Baltimore,D. and Darnell,J. (1995) Molecular Cell Biology, 3rd Edn. Scientific American Books, New York, NY.