Prediction of protein function and pathways in the genome era

Cellular and Molecular Life Sciences

Volumn 61, Issue 7-8, 2004, Pages 930-944

  Gabaldon T ^a   Huynen, M A ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Comparative genomics; Function prediction; Genomic context; Orthology; Pathways; RNase L inhibitor

Indexed keywords

PROTEIN; RIBONUCLEASE L; RIBOSOME RNA;

CHROMOSOME ANALYSIS; COEVOLUTION; COMPARATIVE GENE MAPPING; CONSERVATION GENETICS; EUKARYOTE; EVOLUTIONARY HOMOLOGY; GENE FUNCTION; GENE FUSION; GENE LIBRARY; GENE MAPPING; GENE SEQUENCE; GENOME; HUMAN; METABOLISM; NONHUMAN; ORTHOLOGY; PARALOGY; PHYLOGENY; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN METABOLISM; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; ARTIFICIAL GENE FUSION; ATP-BINDING CASSETTE TRANSPORTERS; BASE SEQUENCE; CHAPERONINS; CHROMOSOMES; EVOLUTION, MOLECULAR; GENOME; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEINS; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT;

EUKARYOTA; PROKARYOTA;

EID: 2442423854     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00018-003-3387-y     Document Type: Review

References (147)

1. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512
2. van Nimwegen E. (2003) Scaling laws in the functional content of genomes. Trends Genet. 19: 479-484
3. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J. and Wheeler D. L. (2003) GenBank. Nucleic Acids Res 31: 23-27
4. Schena M., Shalon D., Davis R. W and Brown P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470
5. Lockhart D. J., Dong H., Byrne M. C., Follettie M. T., Gallo M. V, Chee M. S. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14: 1675-1680
6. Chien C. T., Bartel P. L., Sternglanz R. and Fields S. (1991) The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl. Acad. Sci. USA 88: 9578-9582
7. Fire A., Xu S., Montgomery M. K., Kostas S. A., Driver S. E. and Mello C. C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811
8. Kamath R. S. and Ahringer J. (2003) Genome-wide RNAi screening in Caenorhabditis elegans. Methods 30: 313-321
9. S. Vidan and M. Snyder (2001) Large-scale mutagenesis: yeast genetics in the genome era. Curr. Opin. Biotechnol. 12: 28-34
10. Galperin M. Y. and Koonin E. V. (2000) Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18: 609-613
11. Iliopoulos I., Tsoka S., Andrade M. A., Janssen P., Audit B., Tramontano A. et al. (2001) Genome sequences and great expectations. Genome Biol. 2: interactions 0001.1-0001.3
12. Huynen M., Snel B., Lathe W., 3rd and Bork P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10: 1204-1210
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. Fitch W. M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99-113
15. Teichmann S. A. (2002) The constraints protein-protein interactions place on sequence divergence. J. Mol. Biol. 324: 399-407
16. Boeckmann B., Bairoch A., Apweiler R., Blatter M. C., Estreicher A., Gasteiger E. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31: 36-370
17. Smith T. F. and Waterman M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197
18. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402
19. Park J., Karplus K., Barrett C., Hughey R., Haussler D.,. Hubbard T et al. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284: 1201-1210
20. Baldi P., Chauvin Y., Hunkapiller T. and McClure M. A. (1994) Hidden Markov models of biological primary sequence information. Proc. Natl. Acad. Sci. USA 91: 1059-1063
21. Letunic I., Goodstadt L., Dickens N. J., T. Doerks, Schultz J., Mott R. et al. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30: 242-244
22. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S. R. et al. (2002) The Pfam protein families database. Nucleic Acids Res. 30: 276-280
23. Mulder N. J., Apweiler R., Attwood T. K., Bairoch A., Bateman A., Binns D. et al. (2002) InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform. 3: 225-235
24. Copley R. R., Doerks T., Letunic I. and Bork P. (2002) Protein domain analysis in the era of complete genomes. FEBS Lett. 513: 129-134
25. Huynen M. A. and Bork P. (1998) Measuring genome evolution. Proc. Natl. Acad. Sci. USA 95: 5849-5856
26. Tatusov R. L., Natale D. A,. Garkavtsev I. V, Tatusova T. A., Shankavaram U. T., Rao B. S. et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 22-28
27. Sonnhammer E. L. and Koonin E. V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18: 619-620
28. Lespinet O., Wolf Y. I., Koonin E. V. and Aravind L. (2002) The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12: 1048-1059
29. Tatusov R. L., Fedorova N. D., Jackson J. J., Jacobs A. R., Kiryutin B., Koonin E. V. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41
30. Eisen J. A. and Fraser C. M. (2003) Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707
31. Saier M. H., Jr., Eng B. H., Fard S., Garg J., Haggerty D. A., Hutchinson W. J. et al. (1999) Phylogenetic characterization of novel transport protein families revealed by genome analyses. Biochim. Biophys. Acta 1422: 1-56
32. Eisen J. A., Sweder K. S. and Hanawalt P. C. (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23: 2715-2723
33. Storm C. E. and Sonnhammer E. L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18: 92-99
34. Yuan Y. P., Eulenstein O., Vingron M. and Bork P. (1998) Towards detection of orthologues in sequence databases. Bioinformatics 14: 285-289
35. Arvestad L., Berglund A. C., Lagergren J. and Sennblad B. (2003) Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19 Suppl. 1: 17-115
36. van Noort V., Snel B. and Huynen M. A. (2003) Predicting gene function by conserved co-expression. Trends Genet. 19: 238-242
37. Snel B., Bork P. and Huynen M. (2000) Genome evolution. Gene fusion versus gene fission. Trends Genet. 16: 9-11
38. Welch G. R. and Easterby J. S. (1994) Metabolic channeling versus free diffusion: transition-time analysis. Trends Biochem. Sci. 19: 193-197
39. Burns D. M., Horn V., Paluh J. and Yanofsky C. (1990) Evolution of the tryptophan synthetase of fungi. Analysis of experimentally fused Escherichia coli tryptophan synthetase alpha and beta chains. J. Biol. Chem. 265: 2060-2069
40. 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
41. Yanai I., Derti A. and DeLisi C. (2001) Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. USA 98: 7940-7945
42. Tsoka S. and Ouzounis C. A. (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat. Genet. 26: 141-142
43. Yanofsky C. (1984) Comparison of regulatory and structural regions of genes of tryptophan metabolism. Mol. Biol. Evol. 1: 143-161
44. Mushegian A. R. and Koonin E. V. (1996) Gene order is not conserved in bacterial evolution. Trends Genet 12: 289-290
45. Watanabe H., Mori H., Itoh T. and Gojobori T. (1997) Genome plasticity as a paradigm of eubacteria evolution. J. Mol. Evol. 44 Suppl. 1: S57-64
46. Wolf Y. I., Rogozin I. B., Kondrashov A. S. and Koonin E. V. (2001) Genome alignment, evolution of prokaryotic genome organization and prediction of gene function using genomic context. Genome Res. 11: 356-372
47. 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
48. Overbeek R. F., D'Souza M., Pusch G. D. and Maltsev N. (1998) Use of contiguity on the chromosome to infer functional coupling. In Silico Biol. 2: 93-108
49. 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
50. 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
51. Blumenthal T. (1998) Gene clusters and polycistronic transcription in eukaryotes. Bioessays 20: 480-487
52. Spieth J., Brooke G., Kuersten S., Lea K. and Blumenthal T. (1993) Operons in C. elegans: polycistronic mRNA precursors are processed by trans-splicing of SL2 to downstream coding regions. Cell 73: 521-532
53. Lee J. M. and Sonnhammer E. L. (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 13: 875-882
54. Hurst L. D., Williams E. J. and Pal C. (2002) Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet. 18: 604-606
55. Huynen M. A. and Snel B. (2003) Exploiting the variation in the genomic associations of genes to predict pathways and reconstruct their evolution. In: Frontiers in Computational Genomics, pp. 145-166, Galperin M. Y. and Koonin E. V. (eds), Caister Academic Press, Norfolk, UK
56. Huynen M. A., Snel B. and Bork P. (2001) Inversions and the dynamics of eukaryotic gene order. Trends Genet. 17: 304-306
57. Bobik T. A. and Rasche M. E. (2001) Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. J. Biol. Chem. 276: 37194-37198
58. Pellegrini M., M. Marcotte E., 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
59. Huynen M. A. and Snel B. (2000) Gene and context: integrative approaches to genome analysis. Adv. Protein Chem. 54: 345-379
60. Gaasterland T. and Ragan M. A. (1998) Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb. Comp. Genomics 3: 199-217
61. Huynen M., Snel B.,. Lathe W and. Bork P (2000) Exploitation of gene context. Curr. Opin. Struct. Biol. 10: 366-370
62. Wu J., Kasif S. and DeLisi C. (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19: 1524X-1530
63. Campuzano V., Montermini L., Molto M. D., Pianese L., Cossee M., Cavalcanti F. et al. (1996) Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion. Science 271: 1423-1427
64. Huynen M. A., Snel B., Bork P. and Gibson T. J. (2001) The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. Hum. Mol. Genet. 10: 2463-2468
65. Muhlenhoff U., Richhardt N., Ristow M., Kispal G. and Lill R. (2002) The yeast frataxin homolog Yfh1p plays a specific role in the maturation of cellular Fe/S proteins. Hum. Mol. Genet. 11: 2025-2036
66. Chen O. S., Hemenway S. and Kaplan J. (2002) Inhibition of Fe-S cluster biosynthesis decreases mitochondrial iron export: evidence that Yfh1p affects Fe-S cluster synthesis. Proc. Natl. Acad. Sci. USA 99: 12321-12326
67. Duby G., Foury F., Ramazzotti A., Herrmann J. and Lutz T. (2002) A non-essential function for yeast frataxin in iron-sulfur cluster assembly. Hum. Mol. Genet. 11: 2635-2643
68. Zheng Y., Roberts R. J. and Kasif S. (2002) Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol. 3: research 0060.1-0060.9
69. Liberles D. A., Thoren A., von Heijne G. and Elofsson A. (2002) The use of phylogenetic profiles for gene prediction. Current Genomics 3: 131-137
70. 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
71. Koonin E. V., Mushegian A. R. and Bork P. (1996) Non-orthologous gene displacement. Trends Genet. 12: 334-336
72. Myllykallio H., Lipowski G., Leduc D., Filee J., Forterre P. and Liebl U. (2002) An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297: 105-107
73. Morett E., Korbel J. O., Rajan E., Saab-Rincon G., Olvera L., Olvera M. et al. (2003) Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat. Biotechnol. 21: 790-795
74. Snel B., Bork P. and Huynen M. A. (1999) Genome phylogeny based on gene content. Nat. Genet. 21: 108-110
75. Perna N. T., Plunkett G., 3rd, Burland V., Mau B., Glasner J. D., Rose D. J. et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529-533
76. Blattner F. R., Plunkett G., 3rd, Bloch C. A., Perna N. T., Burland V., Riley M. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474
77. Buchrieser C., Rusniok C., Kunst F., Cossart P. and Glaser P. (2003) Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: clues for evolution and pathogenicity. FEMS Immunol. Med. Microbiol. 35: 207-213
78. Aravind L., Watanabe H., Lipman D. J. and Koonin E. V. (2000) Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc. Natl. Acad. Sci. USA 97: 11319-11324
79. 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
80. Fryxell K. J. (1996) The coevolution of gene family trees. Trends Genet. 12: 364-369
81. Goh C. S., Bogan A. A., Joachimiak M., Walther D. and Cohen F. E. (2000) Coevolution of proteins with their interaction partners. J. Mol. Biol. 299: 283-293
82. Hughes A. L. and Yeager M. (1999) Coevolution of the mammalian chemokines and their receptors. Immunogenetics 49: 115-124
83. Pazos F. and Valencia A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14: 609-614
84. Valencia A. and Pazos F. (2003) Prediction of protein-protein interactions from evolutionary information. Methods Biochem. Anal. 44: 411-426
85. Ramani A. K. and Marcotte E. M. (2003) Exploiting the coevolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327: 273-284
86. Ortiz A. R., Kolinski A., Rotkiewicz P., Ilkowski B. and Skolnick J. (1999) Ab initio folding of proteins using restraints derived from evolutionary information. Proteins Suppl. 3: 177-185
87. Gobel U., Sander C., Schneider R. and Valencia A. (1994) Correlated mutations and residue contacts in proteins. Proteins 18: 309-317
88. Pazos F., Helmer-Citterich M., Ausiello G. and Valencia A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271: 511-523
89. Pazos F. and Valencia A. (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219-227
90. Aloy P. and Russell R. B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. USA 99: 5896-5901
91. Mendez R., Leplae R., De Maria L. and Wodak S. J. (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52: 51-67
92. Velculescu V. E., Zhang L., Vogelstein B. and Kinzler K. W. (1995) Serial analysis of gene expression. Science 270: 484-487
93. Grigoriev A. (2001) 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. 29: 3513-3519
94. Jansen R., Greenbaum D. and Gerstein M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res. 12: 37-46
95. Ge H.,. Liu Z, Church G. M. and Vidal M. (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29: 482-486
96. DeRisi J. L., Iyer V. R. and Brown P. O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686
97. 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. Nat. Genet 31: 255-265
98. Eisen M. B., Spellman P. T., Brown P. O. and Botstein D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863-14868
99. Niehrs C. and Pollet N. (1999) Synexpression groups in eukaryotes. Nature 402: 483-487
100. Wen X., Fuhrman S., Michaels G. S., Carr D. B., Smith S., Barker J. L. et al. (1998) Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci. USA 95: 334-339
101. Hughes T. R., Marton M. J., Jones A. R., Roberts C. J., Stoughton R., Armour C. D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126
102. Noordewier M. O. and Warren P. V. (2001) Gene expression microarrays and the integration of biological knowledge. Trends Biotechnol. 19: 412-415
103. Teichmann S. A. and Babu M. M. (2002) Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol 20: 407-10; discussion 410
104. Stuart J. M, Segal E., Koller D. and Kim S. K. (2003) A gene coexpression network for global discovery of conserved genetic modules. Science 302: 249-255
105. Kelley B. P., Sharan R., Karp R. M., Sittler T., Root D. E., Stockwell B. R. et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA 100: 11394-11399
106. Yanai I., Mellor J. C. and DeLisi C. (2002) Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 18: 176-179
107. Jansen R., Lan N., Qian J. and Gerstein M. (2002) Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics 2: 71-81
108. Huynen M. A., Snel B., Mering C. and Bork P. (2003) Function prediction and protein networks. Curr. Opin. Cell Biol. 15: 191-198
109. von Mering C., Krause R., Snel B., Cornell M., Oliver S. G., Fields S. et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403
110. Xenarios I., Salwinski L., Duan X. J., Higney P., Kim S. M. and Eisenberg D. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303-305
111. Zanzoni A., Montecchi-Palazzi L., Quondam M., Ausiello G., Helmer-Citterich M. and Cesareni G. (2002) MINT: a Molecular INTeraction database. FEBS Lett. 513: 135-140
112. Bader G. D., Betel D. and Hogue C. W. (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31: 248-250
113. 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
114. Hill D. P., Blake J. A., Richardson J. E. and Ringwald M. (2002) Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res. 12: 1982-1991
115. Tatusov R. L., Galperin M. Y., Natale D. A. and Koonin E. V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36
116. 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
117. Matte-Tailliez O., Zivanovic Y. and Forterre P. (2000) Mining archaeal proteomes for eukaryotic proteins with novel functions: the PACE case. Trends Genet. 16: 533-536
118. Jeong H., Mason S. P., Barabasi A. L. and Oltvai Z. N. (2001) Lethality and centrality in protein networks. Nature 411: 41-42
119. 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
120. Snel B., Bork P. and Huynen M. A. (2002) The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA 99: 5890-5895
121. Spirin V. and Mirny L. A. (2003) Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. USA 100: 12123-12128
122. Vazquez A., Flammini A., Maritan A. and Vespignani A. (2003) Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 21: 697-700
123. Goldberg D. S. and. Roth F. P (2003) Assessing experimentally derived interactions in a small world. Proc. Natl. Acad. Sci. USA 100: 4372-4376
124. Jeong H., Tombor B., Albert R., Oltvai Z. N. and Barabasi A. L. (2000) The large-scale organization of metabolic networks. Nature 407: 651-654
125. Maslov S. and Sneppen K. (2002) Specificity and stability in topology of protein networks. Science 296: 910-913
126. Ma H. and Zeng A. P. (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19: 270-277
127. Aloy P. and Russell R. B. (2002) Potential artefacts in protein-interaction networks. FEBS Lett. 530: 253-254
128. Barabasi A. L. and Albert R. (1999) Emergence of scaling in random networks. Science 286: 509-512
129. Pastor-Satorras R., Smith E. and Sole R. V. (2003) Evolving protein interaction networks through gene duplication. J. Theor. Biol. 222: 199-210
130. Paley S. M. and Karp P. D. (2002) Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics 18: 715-724
131. Overbeek R., Larsen N., Pusch G. D., D'Souza M., Selkov E., Jr., Kyrpides N. et al. (2000) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28: 123-125
132. Schilling C. H.,. Covert M. W, Famili, I., Church G. M., Edwards J. S. and Palsson B. O. (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184: 4582-4593
133. Schilling C. H. and Palsson B. O. (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol. 203: 249-283
134. Dandekar T., Schuster S., Snel B., Huynen M. and Bork P. (1999) Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J 343 Pt 1: 115-124
135. 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
136. Becker K., Schirmer M., Kanzok S. and Schirmer R. H. (1999) Flavins and flavoenzymes in diagnosis and therapy. Methods Mol. Biol. 131: 229-245
137. Bisbal C., Martinand C., Silhol M., Lebleu B. and Salehzada T. (1995) Cloning and characterization of a RNAse L inhibitor. A new component of the interferon-regulated 2-5A pathway. J. Biol. Chem. 270: 13308-13317
138. Zimmerman C., Klein K. C., Kiser P. K., Singh A. R., Firestein B. L., Riba S. C. et al. (2002) Identification of a host protein essential for assembly of immature HIV-1 capsids. Nature 415: 88-92
139. Fromme J. C. and Verdine G. L. (2003) Structure of a trapped endonuclease III-DNA covalent intermediate. EMBO J. 22: 3461-3471
140. Porello S. L., Cannon M. J. and David S. S. (1998) A substrate recognition role for the [4Fe-4S]2+ cluster of the DNA repair glycosylase MutY. Biochemistry 37: 6465-6475
141. Strong M., Mallick P., Pellegrini M., Thompson M. J. and Eisenberg D. (2003) Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 4: R59
142. Kromer W. J. and Arndt E. (1991) Halobacterial S9 operon. Three ribosomal protein genes are cotranscribed with genes encoding a tRNA(Leu), the enolase and a putative membrane protein in the archaebacterium Haloarcula (Halobacterium) marismortui. J. Biol. Chem. 266: 24573-24579
143. Santangelo G. M. and Tornow J. (1990) Efficient transcription of the glycolytic gene ADH1 and three translational component genes requires the GCR1 product, which can act through TUF/GRF/RAP binding sites. Mol Cell Biol 10: 859-862
144. Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M. and Yuan Y. (1998) Predicting function: from genes to genomes and back. J. Mol. Biol. 283: 707-725
145. (2001) Creating the gene ontology resource: design and implementation. Genome Res. 11: 1425-1433
146. Snel B., Lehmann G., Bork P. and Huynen M. A. (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 28: 3442-3444
147. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T. J., Higgins D. G. et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31: 3497-3500