Predicting protein-protein interactions from protein domains using a set cover approach

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 4, Issue 1, 2007, Pages 78-87

  Huang, Chengbang ^a   Morcos, Faruck ^a   Kanaan, Simon P ^b   Wuchty, Stefan ^c   Chen, Danny Z ^a   Izaguirre, Jesús A ^a  

^a University of Notre Dame   (United States)

^b ACCENTURE   (United States)

^c NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Bioinformatics (genome or protein) databases; Biology; Computations on discrete structures; Genetics; Graph algorithms

Indexed keywords

COMPUTATIONS ON DISCRETE STRUCTURES; GENETICS; GRAPH ALGORITHMS;

ALGORITHMS; BIOINFORMATICS; DATABASE SYSTEMS; GENETIC ENGINEERING; INTERFACES (MATERIALS); YEAST;

PROTEINS;

SACCHAROMYCES CEREVISIAE;

ATP DEPENDENT 26S PROTEASE; PROTEASOME; PROTEIN; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE PROTEIN; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; INTERNET; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; STATISTICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; INTERNET; LIKELIHOOD FUNCTIONS; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOMICS; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 33847720776     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.1001     Document Type: Conference Paper

References (53)

1. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki, "A Comprehensive Two-Hybrid Analysis to Explore the Yeast Protein Interactome," Proc. Nat'l Academy of Science USA, vol. 98, no. 8, pp. 4569-4574, 2001.
2. T. Ito, K. Tashiro, S. Muta, R. Ozawa, T. Chibba, M. Nishizawa, K. Yamamoto, S. Kuhara, and Y. Sakaki, "Towards 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. Nat'l Academy of Science USA, vol. 97, no. 3, pp. 1143-1147, 2000.
3. B. Schwikowski, P. Uetz, and S. Fields, "A Network of Protein-Protein Interactions in Yeast," Nature Biotechnology, vol. 18, pp. 1257-1261, 2000.
4. P. Uetz, L. Giot, G. Cagney, T. Mansfield, R. Judson, J. Knight, D. Lockshorn, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, and J. Rothberg, "A Comprehensive Analysis of Protein-Protein Interactions of Saccharomyces cerevisiae," Nature, vol. 403, pp. 623-627, 2000.
5. J.S. Bader, D. Chaudhuri, and J. Chant, "Gaining Confidence in High-Throughput Protein Interaction Networks," Nature Biotechnology, vol. 22, pp. 78-85, 2004.
6. P. Bork, L. Jensen, C. von Mering, A. Ramani, and E. Marcotte, "Protein Interaction Networks from Yeast to Human," Current Opinion on Structural Biology, vol. 14, pp. 292-299, 2004.
7. M. Vidai, "Interactome Modelling,'"" FEBS Letters, vol. 579, pp. 1834-1838, 2005.
8. D. LaCount, M. Vignali, R. Chetlier, A. Phansalkar, R. Bell, J. Hesselberth, L. Schoenfeld, S.S.I. Ota, C. Kurschner, S. Fields, and R. Hughes, "A Protein Interaction Network of the Malaria Parasite Plasmodium falciparum," Nature, vol. 438, pp. 103-107, 2005.
9. A. Walhout, R. Sordella, X. Lu, J. Hartley, G. Temple, M. Brasch, N. Thierry-Mieg, and M. Vidal, "Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development," Science, vol. 287, pp. 116-122, 2000.
10. S. Li, C. Armstrong, N. Bertin, H. Go, S. Milstein, M. Boxem, P.-O. Vidalain, J.-D. Han, A. Chesneau, and T. Ha, "A Map of the Interactome Network of the Metazoan C. Elegans," Science, vol. 303, pp. 540-543, 2004.
11. L. Giot, J. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y. Hao, C. Ooi, B. Godwin, E. Vitols, G. Vijayadamodar, P. Pochart, H. Machineni, M. Welsh, Y. Kong, B. Zerhusen, R. Malcolm, Z. Varrone, A. Collis, M. Minto, S. Burgess, L. McDaniel, E. Stimpson, F. Spriggs, J. Williams, K. Neurath, N. Ioime, M. Agee, E. Voss, K. Furtak, R. Renzulli, N. Aanensen, S. Carrolla, E. Bickelhaupt, Y. Lazovatsky, A. DaSilva, J. Zhong, C. Stanyon, R. Finley Jr., K. White, M. Braverman, T. Jarvie, S. Gold, M. Leach, J. Knight, R. Shimkets, M. McKenna, J. Chant, and J. Rothberg, "A Protein Interaction Map of Drosophila melanogaster," Science, vol. 302, pp. 1727-1736, 2004.
12. J.-F. Ruai et al., "Towards a Proteome-Scale Map of the Human Protein-Protein Interaction Network," Nature, vol. 437, pp. 1173-1178, 2005.
13. A. Enright, T. Iliopoulos, N. Kyrpidcs, and C. Ouzounis, "Protein Interaction Maps for Complete Genomes Based on Gene Fusion Events," Nature, vol. 402, pp. 86-90, 1999.
14. E. Marcotte, M. Pellegrini, M., Thompson, T. Yeates, and D. Eisenberg, "A Combined Algorithm for Genomewide Prediction of Protein Function," Nature, vol. 402, pp. 83-86, 1999.
15. M. Pellegrini, E. Marcotte, M. Thompson, D. Eisenberg, and T. Yeates, "Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles," Proc. Nat'l Academy of Sciences USA, vol. 96, pp. 4285-4288, 1999.
16. E. Marcotte, M. Pellegrini, H.-L. Ng, D. Rice, T. Yeates, and D. Eisenberg, "Detecting Protein Function and Protein-Protein Interactions from Genome Sequences," Science, vol. 285, pp. 751-753, 1999.
17. D. Ekman, J.F. -S. A. K. Björklund, and E. Elofsson, "Multi-Domain Proteins in the Three Kingdoms of Life: Orphan Domains and Other Unassigned Regions," J. Molecular Biology, vol. 348, pp. 231-243, 2005.
18. J. Wojcik and V. Schächter, "Protein-Protein Interaction Map Inference Using Interacting Domain Profile Pairs," Bioinfornmtics, vol. 17, pp. 296S-305S, 2001.
19. J. Espadalcr, R.J.O. Romero-Isart, and B. Oliva, "Prediction of Protein-Protein Interactions Using Distant Conservation of Sequence Patterns and Structure Relationships," Bioinformatics, vol. 21, pp. 3360-3368, 2005.
20. P. Aloy, B. Böttcher, H. Ceulemans, C. Leutwein, C. Mellwig, S. Fischer, A.-C. Gavin, P. Bork, G. Superti-Furga, L. Serrano, and R. Russell, "Structure-Based Assembly of Protein Complexes in Yeast," Science, vol. 303, pp. 2026-2029, 2004.
21. A. Stein, R. Russell, and P. Aloy, "3did: Interacting Protein Domains of Known Three-Dimensional Structure," Nucleic Acids Research, vol. 33, pp. D413-D417, 2005.
22. M. Deng, S. Mehta, F. Sun, and T. Cheng, "Inferring Domain-Domain Interactions from Protein-Protein Interactions," Genome Research, vol. 12, pp. 1540-1548, 2002.
23. I. Iossifov, M. Krauthammer, C. Friedman, V. Hatzivassiloglou, J. Bader, K. White, and A. Rzhetsky, "Probabilistic Inference of Molecular Networks from Noisy Data Sources," Bioinformatics, vol. 20, pp. 1205-1213, 2004.
24. E. Sprinzak and H. Margalit, "Correlated Sequence-Signature as Markers of Protein-Protein Interaction," J. Molecular Biology, vol. 311, pp. 681-692, 2001.
25. S.M. Gomez, W.S. Noble, and A. Rzhetsky, "Learning to Predict Protein-Protein Interactions from Protein Sequences," Bioinformatics, vol. 19, pp. 1875-1881, 2003.
26. D. Han, H.-S. Kim, J. Seo, and W. Jang, "A Domain Combination Based Probabilistic Framework for Protein-Protein Interaction Prediction," Genome Informatics, vol. 14, pp. 250-259, 2003.
27. D. Goldberg and F. Roth, "Assessing Experimentally Derived Interactions in a Small-World," Proc. Nat'l Academy of Sciences USA, vol. 100, no. 8, pp. 4372-4376, 2003.
28. R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N. Krogan, S. Chung, A. Emili, M. Snyder, J. Greenblatt, and M. Gerstein, "A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data," Science, vol. 302, pp. 449-453, 2003.
29. N. Nariai, S. Kim, S. Imoto, and S. Miyano, "Using Protein-Protein Interactions for Refining Gene Networks Estimated from Micro-array Data by Bayesian Networks," Proc. Pacific Symp. Biocomputing, pp. 336-347, 2004.
30. I. Albert and R. Albert, "Conserved Network Motifs Allow Protein-Protein Interaction Prediction," Bioinformatics, vol. 20, pp. 3346-3352, 2004.
31. S. Gomez, S. Lo, and A. Rhetsky, "Probabilistic Prediction of Unknown Metabolic and Signal Transduction Networks," Genetics, vol. 159, pp. 1291-1298, 2001.
32. A. Tong et al., "A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules," Science, vol. 295, pp. 321-324, 2002.
33. D. Rhodes, S. Tomlins, S. Varambally, V. Mahavisno, T. Barrette, S. Kalyana-Sundaram, D. Ghosh, A. Pandey, and A. Chinnaiyan, "Probabilistic Model of the Human Protein-Protein Interaction Network," Nature Biotechnology, vol. 23, pp. 951-959, 2005.
34. A. Bateman, L. Coin, R. Durbin, R. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E. Sonnhammer, D. Studholme, C. Yeats, and S. Eddy, "The Pfam Protein Families Database," Nucleic Acids Research, vol. 32, pp. D138-D141, 2004.
35. A. Zanzoni, L. Montecchi-Palazzi, M. Quondam, G. Ausicllo, M. Helmer-Citterich, and G. Cesareni, "MINT - A Molecular INTeraction Database," FEBS Letters, vol. 513, pp. 135-140, 2002.
36. H.W. Mewes, U.B. D. Frishman, G. Mannhaupt, K. Mayer, M. Mokrejs, M.M. B. Morgenstern, S. Rudd, and B. Weil, "MIPS: A Database for Genomes and Protein Sequences," Nucleic Acids Research, vol. 30, pp. 31-34, 2002.
37. G. Bader, I. Donaldson, C. Wolting, B. Ouellette, T. Pawson, and C. Hogue, "BIND - the Biomolecular Interaction Network Database," Nucleic Acids Research, vol. 29, pp. 242-245, 2001.
38. J. Mellor, I. Yanai, K. Clodfelter, J. Mintseris, and C. DeLisi, "Predictome: a Database of Putative Functional Links between Proteins," Nucleic Acids Research, vol. 30, pp. 306-309, 2002.
39. C. vonMering, M. Huynen, D. Jaeggi, P.B.S. Schmidt, and B. Snel, "STRING: a Database of Predicted Functional Associations between Proteins," Nucleic Acids Research, vol. 31, pp. 258-261, 2003.
40. I. Xenarios, L. Salwinski, X. Duan, P. Higney, S.-M. Kim, and D. Eisenberg, "DIP, the Database of Interacting Proteins: A Research Tool for Studying Cellular Networks of Protein Interactions," Nucleic Acids Research, vol. 30, pp. 303-305, 2002.
41. R. Krause, C. vonMering, and P. Bork, "A Comprehensive Set of Protein Complexes in Yeast: Mining Large Scale Protein-Protein Interaction Screens," Bioinformatics, vol. 19, pp. 1901-1908, 2003.
42. Y. Ho et al., "Systematic Identification of Protein Complexes in Saccharomyces cerevisiae by Mass Spectrometry," Nature, vol. 415, pp. 180-183, 2002.
43. A. Gavin, M. Bösche, R. Krause, P. Grandi, M. Marazioch, A. Bauer, J. Schultz, J. Rick, A.-M. Michon, C.-M. Cruciat, M. Remor, C. Böfert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Basluck, B. Huhse, C. Leutwein, M.-A. Heurtier, R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeestcr, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga, "Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes," Nature, vol. 415, pp. 141-147, 2002.
44. F. Corpet, F. Servant, J. Gouzy, and D. Kahn, "ProDom and ProDom-CG: Tools for Protein Domain Analysis and Whole Genome Comparisons," Nucleic Acids Research, vol. 28, no. 1, pp. 267-269, 2000.
45. B. Boeckmann, A. Bairoch, R. Apweiler, M.-C. Blatter, A. Estreicher, E. Gasteiger, M. Martin, K. Michoud, C. O'Donovan, I. Phan, S. Pilbout, and M. Schneider, "The SWISS-PROT Protein Knowledgebase and Its Supplement TrEMBL in 2003," Nucleic Acids Research, vol. 31, pp. 365-390, 2003.
46. A. Grigoriev, "A Relationship between Gene Expression and Protein Interactions on the Proteome Scale: Analysis of the Bacteriophage T7 and the Yeast Saccharomyces cerevisiae," Nucleic Acids Research, vol. 29, pp. 3513-3519, 2001.
47. H. Ge, L. Ziu, G. Church, and M. Vidai, "Correlation between Transcriptome and Interactome Mapping Data from Saccharomyces cerevisiae," Nature Genetics, vol. 29, pp. 482-486, 2001.
48. R. Jansen, D. Greenbaum, and M. Gerstein, "Relating Whole-Genome Expression Data with Protein-Protein Interactions," Genome Research, vol. 12, pp. 37-42, 2002.
49. "The Gene Ontology (GO) Database and Information Resource," Nucleic Acids Research, vol. 32, pp. D258-D261,G.O. Consortium, 2004.
50. D. Martin, C. Brun, E. Remy, P. Mouren, D. Thieffry, and B. Jacq, "GOToolBox: Functional Analysis of Gene Data Sets Based on Gene Ontology," Genome Biology, vol. 5, no. 12, pp. 1901-1908, 2004.
51. D.S. Johnson, "Approximation Algorithms for Combinatorial. Problems," J. Computer System Science, vol. 9, pp. 256-278, 1974.
52. T.H. Cormen, C.E. Leiserson, R.L. Rivest, and C. Stein, Introduction to Algorithms, second ed. McGraw-Hill, 2001.
53. C. Huang, "Multiscale Computational Methods for Morphogenesis and Algorithms for Protein-Protein Interaction Inference," PhD dissertation, Dept. of Computer Science and Eng., Univ. of Notre Dame, July 2005, http://etd.nd.edu/ETD-db/theses/available/etd-07212005-085435/.