Predicting physical interactions between protein complexes

Molecular and Cellular Proteomics

Volumn 12, Issue 6, 2013, Pages 1723-1734

  Clancy, Trevor ^a   Rødland, Einar Andreas ^b   Nygard, Ståle ^b   Hovig, Eivind ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPLEX FORMATION; COMPUTER ANALYSIS; HUMAN; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN INTERACTION; STATISTICAL ANALYSIS;

ALGORITHMS; DATABASES, PROTEIN; HUMANS; LIKELIHOOD FUNCTIONS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEIN MULTIMERIZATION; PROTEOME; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84878693986     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O112.019828     Document Type: Article

References (46)

1. Alberts, B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294 (Pubitemid 28093007)
2. Gibson, T. J. (2009) Cell regulation: determined to signal discrete cooperation. Trends Biochem. Sci. 34, 471-482
3. Hartwell, L. H., Hopfield, J. J., Leibler, S., and Murray, A. W. (1999) From molecular to modular cell biology. Nature 402, C47-C52
4. Spirin, V., and Mirny, L. A. (2003) Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. U.S.A. 100, 12123-12128 (Pubitemid 37271525)
5. Brenner, S. (2010) Sequences and consequences. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365, 207-212
6. Han, J.-D., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J., Cusick, M. E., Roth, F. P., and Vidal, M. (2004) Evidence for dynamically organized modularity in the yeast proteinprotein interaction network. Nature 430, 88-93 (Pubitemid 38915230)
7. Malovannaya, A., Lanz, R. B., Jung, S. Y., Bulynko, Y., Le, N. T., Chan, D. W., Ding, C., Shi, Y., Yucer, N., Krenciute, G., Kim, B.-J., Li, C., Chen, R., Li, W., Wang, Y., O'Malley, B. W., and Qin, J. (2011) Analysis of the human endogenous coregulator complexome. Cell 145, 787-799
8. Sprinzak, E., Altuvia, Y., and Margalit, H. (2006) Characterization and prediction of protein-protein interactions within and between complexes. Proc. Natl. Acad. Sci. U.S.A. 103, 14718-14723 (Pubitemid 44527796)
9. Devos, D., and Russell, R. B. (2007) A more complete, complexed, and structured interactome. Curr. Opin. Struct. Biol. 17, 370-377 (Pubitemid 47021365)
10. Malovannaya, A., Li, Y., Bulynko, Y., Jung, S. Y., Wang, Y., Lanz, R. B., O'Malley, B. W., and Qin, J. (2010) Streamlined analysis schema for high throughput identification of endogenous protein complexes. Proc. Natl. Acad. Sci. U.S.A. 107, 2431-2436
11. Gavin, A.-C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M.-A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A.-M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B., and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636
12. Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., Beattie, B., Richards, D. P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M. M., Vlasblom, J., Wu, S., Orsi, C., Collins, S. R., Chandran, S., Haw, R., Rilstone, J. J., Gandi, K., Thompson, N. J., Musso, G., St Onge, P., Ghanny, S., Lam, M. H., Butland, G., Altaf-Ul, A. M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J. S., Ingles, C. J., Hughes, T. R., Parkinson, J., Gerstein, M., Wodak, S. J., Emili, A., and Greenblatt, J. F. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
13. Ewing, R. M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., McBroom-Cerajewski, L., Robinson, M. D., O'Connor, L., Li, M., Taylor, R., Dharsee, M., Ho, Y., Heilbut, A., Moore, L., Zhang, S., Ornatsky, O., Bukhman, Y. V., Ethier, M., Sheng, Y., Vasilescu, J., Abu-Farha, M., Lambert, J. P., Duewel, H. S., Stewart, I. I., Kuehl, B., Hogue, K., Colwill, K., Gladwish, K., Muskat, B., Kinach, R., Adams, S. L., Moran, M. F., Morin, G. B., Topaloglou, T., and Figeys, D. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3, 89
14. Aloy, P., and Russell, R. B. (2002) Potential artefacts in protein-interaction networks. FEBS Lett. 530, 253-254
15. de Lichtenberg, U., Jensen, L. J., Brunak, S., and Bork, P. (2005) Dynamic complex formation during the yeast cell cycle. Science 307, 724-727 (Pubitemid 40194642)
16. Choi, H., Larsen, B., Lin, Z. Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z. S., Tyers, M., Gingras, A. C., and Nesvizhskii, A. I. (2011) SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat. Methods 8, 70-73
17. Gagneur, J., David, L., and Steinmetz, L. M. (2006) Capturing cellular machines by systematic screens of protein complexes. Trends Microbiol. 14, 336-339 (Pubitemid 44108650)
18. Goll, J., and Uetz, P. (2006) The elusive yeast interactome. Genome Biol. 7, 223
19. Mewes, H. W., Frishman, D., Mayer, K. F., Münsterkötter, M., Noubibou, O., Pagel, P., Rattei, T., Oesterheld, M., Ruepp, A., and Stümpflen, V. (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 34, D169-D172
20. Cherry, J. M., Adler, C., Ball, C., Chervitz, S. A., Dwight, S. S., Hester, E. T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S., and Botstein, D. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26, 73-79 (Pubitemid 28295265)
21. Ruepp, A., Waegele, B., Lechner, M., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., and Mewes, H. (2010) CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res. 38, 497-501
22. Pu, S., Wong, J., Turner, B., Cho, E., and Wodak, S. J. (2009) Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 37, 825-831
23. Wang, H., Kakaradov, B., Collins, S. R., Karotki, L., Fiedler, D., Shales, M., Shokat, K. M., Walther, T. C., Krogan, N. J., and Koller, D. (2009) A complex-based reconstruction of the Saccharomyces cerevisiae interactome. Mol. Cell. Proteomics 8, 1361-1381
24. Razick, S., Magklaras, G., and Donaldson, I. M. (2008) iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 9, 405
25. Turner, B., Razick, S., Turinsky, A. L., Vlasblom, J., Crowdy, E. K., Cho, E., Morrison, K., Donaldson, I. M., and Wodak, S. J. (2010) iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database 2010 Oct 12;2010:baq023
26. Schaefer, M. H., Fontaine, J. F., Vinayagam, A., Porras, P., Wanker, E. E., and Andrade-Navarro, M. A. (2012) HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One 7, e31826
27. Patil, A., Nakai, K., and Nakamura, H. (2011) HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 39, D744-D749
28. Ahn, Y.-Y., Bagrow, J. P., and Lehmann, S. (2010) Link communities reveal multiscale complexity in networks. Nature 466, 761-764
29. Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., and Birney, E. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 19, 327-335
30. Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., Cooke, M. P., Walker, J. R., and Hogenesch, J. B. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A. 101, 6062-6067 (Pubitemid 38520528)
31. Bossi, A., and Lehner, B. (2009) Tissue specificity and the human protein interaction network. Mol. Syst. Biol. 5, 260
32. Schlegel, B. P., Green, V. J., Ladias, J. A., and Parvin, J. D. (2000) BRCA1 interaction with RNA polymerase II reveals a role for hRPB2 and hRPB10α in activated transcription. Proc. Natl. Acad. Sci. U.S.A. 97, 3148-3153 (Pubitemid 30183270)
33. Sato, S., Tomomori-Sato, C., Parmely, T. J., Florens, L., Zybailov, B., Swanson, S. K., Banks, C. A., Jin, J., Cai, Y., Washburn, M. P., Conaway, J. W., and Conaway, R. C. (2004) A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol. Cell 14, 685-691 (Pubitemid 38739090)
34. Ruepp, A., Zollner, A., Maier, D., Albermann, K., Hani, J., Mokrejs, M., Tetko, I., Güldener, U., Mannhaupt, G., Münsterkötter, M., and Mewes, H. W. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32, 5539-5545 (Pubitemid 39545671)
35. Pypaert, M., Mundy, D., Souter, E., Labbé, J. C., and Warren, G. (1991) Mitotic cytosol inhibits invagination of coated pits in broken mitotic cells. J. Cell Biol. 114, 1159-1166 (Pubitemid 21909876)
36. Rossé, C., L'Hoste, S., Offner, N., Picard, A., and Camonis, J. (2003) RLIP, an effector of the Ral GTPases, is a platform for Cdk1 to phosphorylate epsin during the switch off of endocytosis in mitosis. J. Biol. Chem. 278, 30597-30604 (Pubitemid 36994564)
37. Rumpf, J., Simon, B., Jung, N., Maritzen, T., Haucke, V., Sattler, M., and Groemping, Y. (2008) Structure of the Eps15-stonin2 complex provides a molecular explanation for EH-domain ligand specificity. EMBO J. 27, 558-569 (Pubitemid 351225680)
38. Kim, J. R., Kim, J., Kwon, Y. K., Lee, H. Y., Heslop-Harrison, P., and Cho, K. H. (2011) Reduction of complex signaling networks to a representative kernel. Sci. Signal. 4, ra35
39. Li, S. S., Xu, K., and Wilkins, M. R. (2011) Visualization and analysis of the complexome network of Saccharomyces cerevisiae. J. Proteome Res., 10, 4744-4756
40. Ding, C., He, X., Meraz, R. F., and Holbrook, S. R. (2004) A unified representation of multiprotein complex data for modeling interaction networks. Proteins 99-108 (Pubitemid 39195886)
41. Lee, S. H., Kim, P.-J., and Jeong, H. (2011) Global organization of protein complexome in the yeast Saccharomyces cerevisiae. BMC Syst. Biol. 5, 126
42. Wilhelm, T., Nasheuer, H.-P., and Huang, S. (2003) Physical and functional modularity of the protein network in yeast. Mol. Cell. Proteomics 2, 292-298
43. Mashaghi, A., Ramezanpour, A., and Karimipour, V. (2004) Investigation of a protein complex network. Eur. Phys. J. B 41, 113-121
44. Valente, A. X., Roberts, S. B., Buck, G. A., and Gao, Y. (2009) Functional organization of the yeast proteome by a yeast interactome map. Proc. Natl. Acad. Sci. U.S.A. 106, 1490-1495
45. Stein, A., Mosca, R., and Aloy, P. (2011) Three-dimensional modeling of protein interactions and complexes is going 'omics. Curr. Opin. Struct. Biol. 21, 200-208
46. Nepusz, T., Yu, H., and Paccanaro, A. (2012) Detecting overlapping protein complexes in protein-protein interaction networks. Nat. Methods 9, 471-472