Accessible protein interaction data for network modeling. Structure of the information and available repositories

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3380 LNBI, Issue , 2005, Pages 1-13

  Gómez, Manuel ^a   Alonso Allende, Ramón ^b   Pazos, Florencio ^c   Grafia, Osvaldo ^d   Juan, David ^d   Valencia, Alfonso ^d  

^a INSTITUTO NACIONAL DE TÉCNICA AEROESPACIAL   (Spain)

^b Bioalma   (Spain)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DATA REDUCTION; MOLECULAR BIOLOGY; MOLECULAR INTERACTIONS; PROBLEM SOLVING; PROTEINS;

AFFINITY PURIFICATION; NETWORK MODELING; PROTEIN INTERACTION DATA; PROTEOMICS;

BIOINFORMATICS;

EID: 36849067008     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-32126-2_1     Document Type: Article

References (103)

1. Uetz, P., et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 2000, 403(6770): p. 623-7.
2. Giot, L., et al., A protein interaction map of Drosophila melanogaster. Science, 2003. 302(5651): p. 1727-36.
3. Rain, J.C., et al., The protein-protein interaction map of Helicobacter pylori. Nature, 2001. 409(6817): p. 211-5.
4. Li, S., et al., A map of the interactome network of the metazoan C. elegans. Science, 2004. 303(5657): p. 540-3.
5. Gavin, A.C., et al., Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 2002. 415(6868): p. 141-7.
6. Landgraf, C., et al., Protein interaction networks by proteome Peptide scanning. PLoS Biol, 2004. 2(1): p. E14.
7. Tong, A.H., et al., A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science, 2002. 295(5553): p. 321-4.
8. Ren, B., et al., Genome-wide location and function of DNA binding proteins. Science, 2000. 290(5500): p. 2306-9.
9. Lee, T.I., et al., Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 2002. 298(5594): p. 799-804.
10. Milo, R., et al., Network motifs: simple building blocks of complex networks. Science, 2002. 298(5594): p. 824-7.
11. Fraser, H.B., et al., Evolutionary rate in the protein interaction network. Science, 2002. 296(5568): p. 750-2.
12. Jeong, H., et al., The large-scale organization of metabolic networks. Nature, 2000. 407(6804): p. 651-4.
13. Jeong, H., et al., Lethality and centrality in protein networks. Nature, 2001. 411(6833): p. 41-2.
14. Maslov, S. and K. Sneppen, Specificity and stability in topology of protein networks. Science, 2002. 296(5569): p. 910-3.
15. Ravasz, E., et al., Hierarchical organization of modularity in metabolic networks. Science, 2002. 297(5586): p. 1551-5.
16. Rives, A.W. and T. Galitski, Modular organization of cellular networks. Proc Natl Acad Sci USA, 2003. 100(3): p. 1128-33.
17. Hoffmann, R. and A. Valencia, Protein interaction: same network, different hubs. Trends Genet, 2003. 19(12): p. 681-3.
18. Milo, R., et al., Superfamilies of evolved and designed networks. Science, 2004. 303(5663): p. 1538-42.
19. Amaral, L.A., et al., Classes of small-world networks. Proc Natl Acad Sci USA, 2000. 97(21): p. 11149-52.
20. Barabasi, A.L. and R. Albert, Emergence of scaling in random networks. Science, 1999. 286(5439): p. 509-12.
21. Snel, B., P. Bork, and M.A. Huynen, The identification of functional modules from the genomic association of genes. Proc Natl Acad Sic USA, 2002. 99(9): p. 5890-5.
22. von Mering, C., et al., Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci USA, 2003. 100(26): p. 15428-33.
23. Wuchty, S., Z.N. Oltvai, and A.L. Barabasi, Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet, 2003. 35(2): p. 176-9.
24. Yook, S.H., Z.N. Oltvai, and A.L. Barabasi, Functional and topological characterization of protein interaction networks. Proteomics, 2004. 4(4): p. 928-42.
25. Fields, S. and O. Song, A novel genetic system to detect protein-protein interactions. Nature, 1989. 340(6230): p. 245-6.
26. Phizicky, E., et al., Protein analysis on a proteomic scale. Nature, 2003. 422(6928): p. 208-15.
27. Stagljar, I. and S. Fields, Analysis of membrane protein interactions using yeast-based technologies. Trends Biochem Sci, 2002. 27(11): p. 559-63.
28. Wehrman, T., et al., Protein-protein interactions monitored in mammalian cells via complementation of beta -lactamase enzyme fragments. Proc Natl Acad Sci USA, 2002. 99(6): p. 3469-74.
29. Ito, T., et al., Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA, 2000. 97(3): p. 1143-7.
30. Ho, Y., et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 2002. 415(6868): p. 180-3.
31. Zhu, H., et al., Global analysis of protein activities using proteome chips. Science, 2001. 293(5537): p. 2101-5.
32. Aloy, P. and R.B. Russell, Potential artefacts in protein-interaction networks. FEBS Lett, 2002. 530(1-3): p. 253-4.
33. Lakey, J.H. and E.M. Raggett, Measuring protein-protein interactions. Curr Opin Struct Biol, 1998. 8(1): p. 119-23.
34. Legrain, P., J. Wojcik, and J.M. Gauthier, Protein-protein interaction maps: a lead towards cellular functions. Trends Genet, 2001. 17(6): p. 346-52.
35. Bader, G.D. and C.W. Hogue, Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol, 2002. 20(10): p. 991-7.
36. von Mering, C., et al., Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 2002. 417(6887): p. 399-403.
37. Grunenfelder, B. and E.A. Winzeler, Treasures and traps in genome-wide data sets: case examples from yeast. Nat Rev Genet, 2002. 3(9): p. 653-61.
38. Wojcik, J. and V. Schachter, Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics, 2001. 17 Suppl 1: p. S296-305.
39. Lappe, M., et al., Generating protein interaction maps from incomplete data: application to fold assignment. Bioinformatics, 2001. 17 Suppl 1: p. S149-56.
40. Matthews, L.R., et al., Identification of potential interaction networks using sequencebased searches for conserved protein-protein interactions or "interologs". Genome Res, 2001.11(12): p. 2120-6.
41. Goffard, N., et al., IPPRED: server for proteins interactions inference. Bioinformatics, 2003. 19(7): p. 903-4.
42. Han, K., et al., HPID: the human protein interaction database {paragraph}. Bioinformatics, 2004.
43. de la Torre, V., et al., iPPI: a web server for protein-protein interactions inference, submited.
44. Aloy, P., et al., The relationship between sequence and interaction divergence in proteins. J Mol Biol, 2003. 332(5): p. 989-98.
45. Valencia, A. and F. Pazos, Computational methods for the prediction of protein interactions. Curr Opin Struct Biol, 2002.12(3): p. 368-73.
46. von Mering, C., et al., STRING: a database of predicted functional associations between proteins. Nucleic Acids Res, 2003. 31(1): p. 258-61.
47. Huynen, M.A., et al., Function prediction and protein networks. Curr Opin Cell Biol, 2003. 15(2): p. 191-8.
48. Deng, M., F. Sun, and T. Chen, Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput, 2003: p. 140-51.
49. Sprinzak, E. and H. Margalit, Correlated sequence-signatures as markers of proteinprotein interaction. J Mol Biol, 2001. 311(4): p. 681-92.
50. Gomez, S.M., S.H. Lo, and A. Rzhetsky, Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics, 2001. 159(3): p. 1291-8.
51. Gomez, S.M. and A. Rzhetsky, Towards the prediction of complete protein-protein interaction networks. Pac Symp Biocomput, 2002: p. 413-24.
52. Yusupov, M.M., et al., Crystal structure of the ribosome at 5.5 A resolution. Science, 2001. 292(5518): p. 883-96.
53. Aloy, P., et al., Structure-based assembly of protein complexes in yeast. Science, 2004. 303(5666): p. 2026-9.
54. Smith, G.R. and M.J. Sternberg, Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol, 2002. 12(1): p. 28-35.
55. Camacho, C.J. and S. Vajda, Protein-protein association kinetics and protein docking. Curr Opin Struct Biol, 2002. 12(1): p. 36-40.
56. Garcia-Ranea, J. A. and A. Valencia, Distribution and functional diversification of the ras superfamily in Saccharomyces cerevisiae. FEBS Lett, 1998.434(3): p. 219-25.
57. Aloy, P. and R.B. Russell, Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA, 2002. 99(9): p. 5896-901.
58. Aloy, P. and R.B. Russell, InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics, 2003. 19(1): p. 161-2.
59. Lu, H., L. Lu, and J. Skolnick, Development of unified statistical potentials describing protein-protein interactions. Biophys J, 2003. 84(3): p. 1895-901.
60. Lu, L., H. Lu, and J. Skolnick, MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins, 2002. 49(3): p. 350-64.
61. Lu, L., et al., Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res, 2003. 13(6A): p. 1146-54.
62. Bauer, B., et al., Effector recognition by the small GTP-binding proteins Ras and Ral. J Biol Chem, 1999. 274(25): p. 17763-70.
63. Hernanz-Falcon, P., et al., Identification of amino acid residues crucial for chemokine receptor dimerization. Nat Immunol, 2004. 5(2): p. 216-23.
64. Morillas, M., et al., Identification of conserved amino acid residues in rat liver carnitine palmitoyltransferase I critical for malonyl-CoA inhibition. Mutation of methionine 593 abolishes malonyl-CoA inhibition. J Biol Chem, 2003. 278(11): p. 9058-63.
65. Azuma, Y., et al., Model of the ran-RCC1 interaction using biochemical and docking experiments. J Mol Biol, 1999. 289(4): p. 1119-30.
66. Renault, L., et al., Structural basis for guanine nucleotide exchange on Ran by the regulator of chromosome condensation (RCC1). Cell, 2001. 105(2): p. 245-55.
67. Hermjakob, H., et al., IntAct: an open source molecular interaction database. Nucleic Acids Res, 2004. 32 Database issue: p. D452-5.
68. Selkov, E., Jr., et al., MPW: the Metabolic Pathways Database. Nucleic Acids Res, 1998. 26(1): p. 43-5.
69. Selkov, E., et al., The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Res, 1996. 24(1): p. 26-8.
70. Overbeek, R., et al., WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res, 2000. 28(1): p. 123-5.
71. Kanehisa, M., et al., The KEGG databases at GenomeNet. Nucleic Acids Res, 2002. 30(1): p. 42-6.
72. Karp, P.D., et al., The EcoCyc Database. Nucleic Acids Res, 2002. 30(1): p. 56-8.
73. van Helden, J., et al., Representing and analysing molecular and cellular function using the computer. Biol Chem, 2000. 381(9-10): p. 921-35.
74. Joshi-Tope, G., et al., The Genome Knowledgebase: A Resource for Biologists and Bioinformaticists. CSHL Symposium 2003, 2003.
75. Wilkinson, M.D. and M. Links, BioMOBY: an open source biological web services proposal. Brief Bioinform, 2002. 3(4): p. 331-41.
76. Andrade, M.A., et al., Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biol Cybern, 1997. 76(6): p. 441-50.
77. Blaschke, C., et al., Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol, 1999: p. 60-7.
78. Friedman, C., et al., GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics, 2001. 17 Suppl 1: p. S74-82.
79. Blaschke, C., L. Hirschman, and A. Valencia, Information extraction in molecular biology. Brief Bioinform, 2002. 3(2): p. 154-65.
80. Xenarios, I., et al., DIP: the database of interacting proteins. Nucleic Acids Res, 2000. 28(1): p. 289-91.
81. Xenarios, I., et al., DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res, 2001. 29(1): p. 239-41.
82. Xenarios, I., et al., DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res, 2002. 30(1): p. 303-5.
83. Gaasterland, T. and M. A. Ragan, Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb Comp Genomics, 1998. 3(4): p. 199-217.
84. Pellegrini, M., et al., Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA, 1999. 96(8): p. 4285-8.
85. Tamames, J., et al., Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol, 1997. 44(1): p. 66-73.
86. Dandekar, T., et al., Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci, 1998. 23(9): p. 324-8.
87. Overbeek, R., et al., Use of contiguity on the chromosome to predict functional coupling. In Silico Biol, 1999. 1(2): p. 93-108.
88. Enright, A.J., et al., Protein interaction maps for complete genomes based on gene fusion events. Nature, 1999. 402(6757): p. 86-90.
89. Marcotte, E.M., et al., Detecting protein function and protein-protein interactions from genome sequences. Science, 1999. 285(5428): p. 751-3.
90. Tsoka, S. and C.A. Ouzounis, Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat Genet, 2000. 26(2): p. 141-2.
91. Fryxell, K.J., The coevolution of gene family trees. Trends Genet, 1996. 12(9): p. 364-9.
92. Pages, S., et al., Species-specificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: prediction of specificity determinants of the dockerin domain. Proteins, 1997. 29(4): p. 517-27.
93. Goh, C.S., et al., Co-evolution of proteins with their interaction partners. J Mol Biol, 2000. 299(2): p. 283-93.
94. Pazos, F. and A. Valencia, Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng, 2001. 14(9): p. 609-14.
95. Ramani, A.K. and E.M. Marcotte, Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol, 2003. 327(1): p. 273-84.
96. Pazos, F., et al., Correlated mutations contain information about protein-protein interaction. J Mol Biol, 1997. 271(4): p. 511-23.
97. Pazos, F. and A Valencia, In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins, 2002. 47(2): p. 219-27.
98. Zanzoni, A., et al., MINT: a Molecular INTeraction database. FEBS Lett, 2002. 513(1): p. 135-40.
99. Bader, G.D., D. Betel, and C.W. Hogue, BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res, 2003. 31(1): p. 248-50.
100. Mewes, H.W., et al., MIPS: a database for genomes and protein sequences. Nucleic Acids Res, 2002. 30(1): p. 31-4.
101. Breitkreutz, B.J., C. Stark, and M. Tyers, The GRID: the General Repository for Interaction Datasets. Genome Biol, 2003. 4(3): p. R23.
102. Bowers, P.M., et al., Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol, 2004. 5(5): p. R35.
103. Mellor, J.C., et al., Predictome: a database of putative functional links between proteins. Nucleic Acids Res, 2002. 30(1): p. 306-9.