Quantifying modularity in the evolution of biomolecular systems

Genome Research

Volumn 14, Issue 3, 2004, Pages 391-397

  Snel, Berend ^a   Huynen, Martijn A ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BIOSYNTHESIS; CATABOLISM; CONTROLLED STUDY; ECOCYC DATABASE; GENE FUNCTION; GENETIC ANALYSIS; GENETIC DATABASE; GENOME ANALYSIS; INTERMETHOD COMPARISON; METABOLISM; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; BACTERIAL GENE; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; EUKARYOTIC CELL; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; PHYLOGENY; PHYSIOLOGY; STATISTICS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES; GENES, ARCHAEAL; GENES, BACTERIAL; METABOLISM; PHYLOGENY;

EID: 1542286745     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1969504     Document Type: Article

References (39)

1. Ettema, T., van der Oost, J., and Huynen, M. 2001. Modularity in the gain and loss of genes: Applications for function prediction. Trends Genet. 17: 485-487.
2. Fitch, W.M. 1970. Distinguishing homologous from analogous proteins Syst. Zool. 19: 99-113.
3. Galperin, M.Y. and Koonin, E.V. 2000. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18: 609-613.
4. 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.
5. 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.
6. Huynen, M.A. and Bork, P. 1998. Measuring genome evolution Proc. Natl. Acad. Sci. 95: 5849-5856.
7. Huynen, M.A., Dandekar, T., and Bork, P. 1999. Variation and evolution of the citric-acid cycle: A genomic perspective. Trends Microbiol. 7: 281-291.
8. Ihmels, J., Friedlander, G, Bergmann, S., Sarig, O., Ziv, Y., and Barkai, N. 2002. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31: 370-377.
9. Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides, C., and Gama-Castro, S. 2002. The EcoCyc Database. Nucleic Acids Res. 30: 56-58.
10. Lawrence, J.G. and Roth, J.R. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143: 1843-1860.
11. Lee, T.L, 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.
12. Manson McGuire, A. and Church, G.M. 2000. Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res. 28: 4523-4530.
13. Marcotte, E.M. 2001. The path not taken. Nat. Biotechnol. 19: 626-627.
14. Mewes, H.W., Frishman, D., Guldener, 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.
15. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., and Alon, U. 2002. Network motifs: Simple building blocks of complex networks. Science 298: 824-827.
16. Moreno-Hagelsieb, G. and Collado-Vides, J. 2002. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics (Suppl. 1) 18: S329-336.
17. Moreno-Hagelsieb, G., Trevino, V., Perez-Rueda, E., Smith, T.F., and Collado-Vides, J. 2001. Transcription unit conservation in the three domains of life: A perspective from Escherichia coli. Trends Genet. 17: 175-177.
18. Morett, E., Korbel, J.O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B., and Bork, P. 2003. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat. Biotechnol. 21: 790-795.
19. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M. 1999. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27: 29-34.
20. 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. 96: 4285-4288.
21. Peregrin-Alvarez, J.M., Tsoka, S., and Ouzounis, C.A. 2003. The phylogenetic extent of metabolic enzymes and pathways. Genome Res. 13: 422-427.
22. Pruess, M., Fleischmann, W., Kanapin, A., Karavidopoulou, Y., Kersey, P., Kriventseva, E., Mittard, V., Mulder, N., Phan, I., Servant, F., et al. 2003. The Proteome Analysis database: A tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31: 414-417.
23. Ramani, A.K. and Marcotte, E.M. 2003. Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327: 273-284.
24. Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N., and Barabasi, A.L. 2002. Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
25. Rives, A.W. and Galitski, T. 2003. Modular organization of cellular networks. Proc. Natl. Acad. Sci. 100: 1128-1133.
26. Rung, J., Schlitt, T., Brazma, A., Freivalds, K., and Vilo, J. 2002. Building and analysing genome-wide gene disruption networks. Bioinformatics (Suppl. 2) 18: S202-210.
27. Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Diaz-Peredo, E., Sanchez-Solano, F., Perez-Rueda, E., Bonavides-Martinez, C., and Collado-Vides, J. 2001. RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29: 72-74.
28. Snel, B., Bork, P., and Huynen, M.A. 1999. Genome phylogeny based on gene content. Nat. Genet. 21: 108-110.
29. Snel, B., Bork, P., and Huynen, M.A. 2000. Genome evolution. Gene fusion versus gene fission. Trends Genet. 16: 9-11.
30. Snel, B., Bork, P., and Huynen, M.A. 2002. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. 99: 5890-5895.
31. Sonnhammer, E.L. and Koonin, E.V. 2002. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18: 619-620.
32. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278: 631-637.
33. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Tatusova, T.A., Shankavaram, U.T., Rao, B.S., Kiryutin, B., Galperin, M.Y., Fedorova, N.D., and Koonin, E.V. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 22-28
34. van Nimwegen, E., Zavolan, M., Rajewsky, N., and Siggia, E.D. 2002. Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics. Proc. Natl. Acad. Sci. 99: 7323-7328.
35. 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.
36. von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., and Snel, B. 2003. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 31: 258-261.
37. Wang, W., Cherry, J.M., Botstein, D., and Li, H. 2002. A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 99: 16893-16898.
38. Winther, R.G. 2001. Varieties of modules: Kinds, levels, origins, and behaviors J. Exp. Zool. 291: 116-129.
39. Wolf, D.M. and Arkin, A.P. 2003. Motifs, modules and games in bacteria. Curr. Opin. Microbiol. 6: 125-134.