Functional modules by relating protein interaction networks and gene expression

Nucleic Acids Research

Volumn 31, Issue 21, 2003, Pages 6283-6289

  Tornow, Sabine ^a   Mewes, H W ^a,b  

^a Natl Res Ctr Environ and Hlth   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CALCULATION; CELL CYCLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; HISTOGRAM; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN INTERACTION; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS;

ALGORITHMS; CELL CYCLE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FUNGAL PROTEINS; GENE EXPRESSION; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; MACROMOLECULAR SUBSTANCES; OPEN READING FRAMES; PROBABILITY; PROTEIN BINDING; STATISTICAL DISTRIBUTIONS; YEASTS;

EID: 0345305369     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg838     Document Type: Article

References (32)

1. Barabasi,A.-L. and Albert,R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
2. Jeong,H., Tombor,B., Albert R., Oltvai,Z.N. and Barabási,A.-L. (2000) The large scale organisation of metabolic networks. Nature, 407, 651-654.
3. Shen-Orr,S., Milo,R., Mangnan,S. and Alon,U. (2002) Network motifs in the transcriptional regulation network of Eschericha coli. Nature Genet., 31, 64-68.
4. Maslov,S. and Sneppen,K. (2002) Specificity and stability in topology of protein networks. Science, 296, 910-913.
5. Hartwell,L.H., Hopfield,J.J., Leibler,S. and Murray,A.W. (1999) From molecular to modular cell biology. Nature, 402 (suppl.), C47-C52.
6. Rives,A.W. and Galitski,T. (2003) Modular organization of cellular networks. Proc. Natl Acad. Sci. USA, 100, 1128-1133.
7. Oltvai,Z.N. and Barabasi,A.-L. (2002) Life's complexity pyramid. Science, 298, 763-764.
8. Lee,T.I., Rinaldi,N.J., Robert,F., Odom,D.T., Bar-Joseph,Z., Gerber,G.K., Hannett,N.M., Harbison,C.T., Thompson,C.M., Simon,I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae, Science, 298, 799-804.
9. Sharan,R. and Shamir,R. (2000) CLICK: a clustering algorithm with application to gene expression analysis. In Proceedings of the 8th ISMB, pp. 260-268.
10. Getz,G., Levine,E., Domany,E. and Zhang,M.Q. (2000) Superparamagnetic clustering of yeast expression profiles. Physica, A279, 457-464.
11. Getz,G., Levine,E. and Domany,E. (2000) Coupled two-way clustering analysis of gene microarray data. Proc. Natl Acad. Sci. USA, 97, 12079-12084.
12. Marcotte,E.M., Pellegrini,M., Thompson,M.J., Yeates,T.O. and Eisenberg,D. (1999) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
13. Ge,H., Church,G.M. and Vidal,M. (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genet., 29, 482-486.
14. Jansen,R., Greenbaum,D. and Gerstein,M. (2002) Relating whole-genome expression data with protein-protein interaction. Genome Res., 12, 37-46.
15. Pavlidis,P. Weston,J., Cai,J. and Noble,W.S. (2002) Learning gene functional classifications from multiple data types. J. Comput. Biol., 9, 474-485.
16. Hanisch,D., Zien,A., Zimmer,R. and Lengauer,T. (2002) Co-clustering of biological networks and gene expression data. Bioinformatics, 18, S145-S154.
17. Mewes,H.W., Frishman,D., Gueldner,U. Mannhaupt,G., Mayer,K., Mokrejs,M., Morgenstern,B. Munsterkotter,M., Rudd,S. and Weil,B. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res., 30, 31-34.
18. Blatt,M, Wiseman,M. and Domany,E. (1996) Superparamagnetic clustering of data. Phys. Rev. Lett., 76, 3251-3255.
19. Domany,E. (1999) Superparamagnetic clustering of data. The definitive solution of an ill posed problem. Physica, A263, 158-169.
20. Vendruscolo,M., Paci,E., Dobson,C.E. and Karplus,M. (2001) Three key residues from critical network in a protein folding transition state. Nature, 409, 641-645.
21. Zhou,X., Kao,M.-C.J. and Wong,W.H. (2002) Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl Acad. Sci. USA, 99, 12783-12788.
22. Spellman,P.T., Sherlock,G., Zhang,M.Q., Iyer,V.R., Anders,K., Eisen,M.B., Brown,P.O., Botstein,D. and Futcher,B. (1998) Comprehensive identification of cell cycle-regulated genes of yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
23. 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. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
24. 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.
25. Agrawal,H. (2002) Extreme self-organization in networks constructed from gene expression data. Phys. Rev. Lett., 89, 268702-268706.
26. Agrawal,H. and Domany,E. (2003) Potts ferromagnets on coexpressed gene networks: identifying maximally stable partitions. Phys. Rev. Lett., 90, 158102-158106.
27. 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.
28. 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.
29. 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.
30. Fellenberg,M., Albermann,K., Zollner,A., Mewes,H.W. and Hani,J. (2000) Integrative analysis of protein interaction data. In Proceedings of the 8th ISMB, pp. 152-161.
31. Swendsen,R.H. and Wang,J.S. (1987) Nonuniversial critical dynamics in Monte Carlo simulations. Phys. Rev. Lett., 58, 86-88.
32. Spirin,V. and Mirny,L.A. Protein complexes and function modules in molecular networks. Proc. Natl Acad. Sci., 2003 Sep 29 [Epub ahead of print], 10.1073/pnas.2032324100.