Viruses and interactomes in translation

Molecular and Cellular Proteomics

Volumn 11, Issue 7, 2012, Pages

  Meyniel Schicklin, Laurène ^a,b   De Chassey, Benoît ^a,b   André, Patrice ^a,b,c   Lotteau, Vincent ^a,b,c  

^a UNIVERSITÉ DE LYON   (France)

^b INSERM   (France)

^c CROIX ROUSSE HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN;

ARTICLE; EPSTEIN BARR VIRUS; HEEL; HEPATITIS C VIRUS; HERPES SIMPLEX VIRUS 1; HUMAN HERPESVIRUS 8; INFLUENZA VIRUS; MATHEMATICAL PARAMETERS; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; VACCINIA VIRUS; VARICELLA ZOSTER VIRUS; VIRUS INFECTION; VIRUS REPLICATION; COMPUTER SIMULATION; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; METABOLISM; PROTEIN ANALYSIS; STATISTICAL MODEL; STATISTICS; VIRUS;

HEPATITIS C VIRUS; HUMAN HERPESVIRUS 1; HUMAN HERPESVIRUS 3; HUMAN HERPESVIRUS 4; HUMAN HERPESVIRUS 8; INFLUENZA A VIRUS; SARS CORONAVIRUS;

COMPUTER SIMULATION; HOST-PATHOGEN INTERACTIONS; HUMANS; MODELS, STATISTICAL; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; VIRAL PROTEINS; VIRUS REPLICATION; VIRUSES;

EID: 84863798004     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M111.014738     Document Type: Article

References (53)

1. Tan, S. L., Ganji, G., Paeper, B., Proll, S., and Katze, M. G. (2007) Systems biology and the host response to viral infection. Nat. Biotechnol. 25, 1383-1389 (Pubitemid 350233127)
2. Calderwood, M. A., Venkatesan, K., Xing, L., Chase, M. R., Vazquez, A., Holthaus, A. M., Ewence, A. E., Li, N., Hirozane-Kishikawa, T., Hill, D. E., Vidal, M., Kieff, E., and Johannsen, E. (2007) Epstein-Barr virus and virus human protein interaction maps. Proc. Natl. Acad. Sci. U.S.A. 104, 7606-7611 (Pubitemid 47185953)
3. Shapira, S. D., Gat-Viks, I., Shum, B. O., Dricot, A., de Grace, M. M., Wu, L., Gupta, P. B., Hao, T., Silver, S. J., Root, D. E., Hill, D. E., Regev, A., and Hacohen, N. (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139, 1255-1267
4. Flajolet, M., Rotondo, G., Daviet, L., Bergametti, F., Inchauspé, G., Tiollais, P., Transy, C., and Legrain, P. (2000) A genomic approach of the hepatitis C virus generates a protein interaction map. Gene 242, 369-379 (Pubitemid 30064523)
5. Dimitrova, M., Imbert, I., Kieny, M. P., and Schuster, C. (2003) Proteinprotein interactions between hepatitis C virus nonstructural proteins. J. Virol. 77, 5401-5414 (Pubitemid 36460954)
6. Fossum, E., Friedel, C. C., Rajagopala, S. V., Titz, B., Baiker, A., Schmidt, T., Kraus, T., Stellberger, T., Rutenberg, C., Suthram, S., Bandyopadhyay, S., Rose, D., von Brunn, A., Uhlmann, M., Zeretzke, C., Dong, Y. A., Boulet, H., Koegl, M., Bailer, S. M., Koszinowski, U., Ideker, T., Uetz, P., Zimmer, R., and Haas, J. (2009) Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog. 5, e1000570
7. Vittone, V., Diefenbach, E., Triffett, D., Douglas, M. W., Cunningham, A. L., and Diefenbach, R. J. (2005) Determination of interactions between tegument proteins of herpes simplex virus type 1. J. Virol. 79, 9566-9571 (Pubitemid 41022299)
8. Lee, J. H., Vittone, V., Diefenbach, E., Cunningham, A. L., and Diefenbach, R. J. (2008) Identification of structural protein-protein interactions of herpes simplex virus type 1. Virology 378, 347-354
9. Uetz, P., Dong, Y. A., Zeretzke, C., Atzler, C., Baiker, A., Berger, B., Rajagopala, S. V., Roupelieva, M., Rose, D., Fossum, E., and Haas, J. (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311, 239-242 (Pubitemid 43108191)
10. Rozen, R., Sathish, N., Li, Y., and Yuan, Y. (2008) Virion-wide protein interactions of Kaposi's sarcoma-associated herpesvirus. J. Virol. 82, 4742-4750 (Pubitemid 351657036)
11. von Brunn, A., Teepe, C., Simpson, J. C., Pepperkok, R., Friedel, C. C., Zimmer, R., Roberts, R., Baric, R., and Haas, J. (2007) Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS One 2, e459
12. Pan, J., Peng, X., Gao, Y., Li, Z., Lu, X., Chen, Y., Ishaq, M., Liu, D., Dediego, M. L., Enjuanes, L., and Guo, D. (2008) Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication. PLoS One 3, e3299
13. McCraith, S., Holtzman, T., Moss, B., and Fields, S. (2000) Genome-wide analysis of vaccinia virus protein-protein interactions. Proc. Natl. Acad. Sci. U.S.A. 97, 4879-4884 (Pubitemid 30238651)
14. Stellberger, T., Häuser, R., Baiker, A., Pothineni, V. R., Haas, J., and Uetz, P. (2010) Improving the yeast two-hybrid system with permutated fusions proteins: the Varicella Zoster Virus interactome. Proteome Sci 8, 8
15. Khadka, S., Vangeloff, A. D., Zhang, C., Siddavatam, P., Heaton, N. S., Wang, L., Sengupta, R., Sahasrabudhe, S., Randall, G., Gribskov, M., Kuhn, R. J., Perera, R., and LaCount, D. J. (2011) A physical interaction network of dengue virus and human proteins. Mol. Cell Proteomics. 10, M111.012187
16. de Chassey, B., Navratil, V., Tafforeau, L., Hiet, M. S., Aublin-Gex, A., Agaugue, S., Meiffren, G., Pradezynski, F., Faria, B. F., Chantier, T., Le Breton, M., Pellet, J., Davoust, N., Mangeot, P. E., Chaboud, A., Penin, F., Jacob, Y., Vidalain, P. O., Vidal, M., André, P., Rabourdin-Combe, C., and Lotteau, V. (2008) Hepatitis C virus infection protein network. Mol. Syst. Biol. 4, 230
17. Zhang, L., Villa, N. Y., Rahman, M. M., Smallwood, S., Shattuck, D., Neff, C., Dufford, M., Lanchbury, J. S., Labaer, J., and McFadden, G. (2009) Analysis of vaccinia virus-host protein-protein interactions: validations of yeast two-hybrid screenings. J. Proteome Res. 8, 4311-4318
18. Navratil, V., de Chassey, B., Meyniel, L., Delmotte, S., Gautier, C., André, P., Lotteau, V., and Rabourdin-Combe, C. (2009) VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res. 37, D661-668
19. Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M., Cusick, M. E., and Cesareni, G. (2009) VirusMINT: a viral protein interaction database. Nucleic Acids Res. 37, D669-673
20. Mason, O., and Verwoerd, M. (2007) Graph theory and networks in Biology. IET Syst. Biol. 1, 89-119 (Pubitemid 46488242)
21. Newman, M. E. J. (2003) The structure and function of complex networks. SIAM Review 45, 167-256
22. Barabási, A. L., and Oltvai, Z. N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113
23. Dyer, M. D., Murali, T. M., and Sobral, B. W. (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog. 4, e32
24. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (Pubitemid 37428274)
25. R Development Core Team (2010) R: A Language and Environment for Statistical Computing.
26. Csardi, G., and Nepusz, T. (2006) The igraph software package for complex network research. InterJournal Complex Systems 1695
27. Clauset, A., Shalizi, C. R., and Newman, M. E. J. (2009) Power-law distributions in empirical data. SIAM Rev. 51, 661-703
28. Maslov, S., and Sneppen, K. (2002) Specificity and stability in topology of protein networks. Science 296, 910-913 (Pubitemid 34464896)
29. Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J., and Russell, R. B. (2003) Protein disorder prediction: implications for structural proteomics. Structure 11, 1453-1459 (Pubitemid 37412427)
30. Haynes, C., Oldfield, C. J., Ji, F., Klitgord, N., Cusick, M. E., Radivojac, P., Uversky, V. N., Vidal, M., and Iakoucheva, L. M. (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput. Biol. 2, e100
31. Rodrigues, F. A., Costa Lda, F., and Barbieri, A. L. (2011) Resilience of protein-protein interaction networks as determined by their large-scale topological features. Mol. Biosyst. 7, 1263-1269
32. Navratil, V., de Chassey, B., Combe, C. R., and Lotteau, V. (2011) When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases. BMC Syst. Biol. 5, 13
33. Barabasi, A. L., and Albert, R. (1999) Emergence of scaling in random networks. Science 286, 509-512
34. López Garcia De Lomana, A., Beg, Q. K., De Fabritiis, G., and Villà-Freixa, J. (2010) Statistical analysis of global connectivity and activity distributions in cellular networks. J. Comput. Biol. 17, 869-878
35. Kuchaiev, O., Stevanović, A., Hayes, W., and Pržulj, N. (2011) GraphCrunch 2: Software tool for network modeling, alignment and clustering. BMC Bioinformatics 12, 24
36. Przulj, N., and Higham, D. J. (2006) Modelling protein-protein interaction networks via a stickiness index. J. R. Soc. Interface 3, 711-716 (Pubitemid 44690101)
37. Albert, R., Jeong, H., and Barabasi, A. L. (2000) Error and attack tolerance of complex networks. Nature 406, 378-382 (Pubitemid 30625551)
38. Newman, M. E. (2003) Mixing patterns in networks. Phys. Rev. E Stat Nonlin Soft Matter Phys. 67, 026126
39. Watts, D. J., and Strogatz, S. H. (1998) Collective dynamics of 'small-world'networks. Nature 393, 440-442
40. Fuxreiter, M., Tompa, P., and Simon, I. (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23, 950-956 (Pubitemid 47050581)
41. Longhi, S. (2010) Structural disorder in viral proteins. Protein Pept. Lett. 17, 930-931
42. Navratil, V., de Chassey, B., Meyniel, L., Pradezynski, F., André, P., Rabourdin- Combe, C., and Lotteau, V. (2010) System-level comparison of protein-protein interactions between viruses and the human type I interferon system network. J. Proteome Res. 9, 3527-3536
43. Bader, S., Kühner, S., and Gavin, A. C. (2008) Interaction networks for systems biology. FEBS Lett. 582, 1220-1224
44. Przulj, N., Corneil, D. G., and Jurisica, I. (2004) Modeling interactome: scale-free or geometric? Bioinformatics 20, 3508-3515 (Pubitemid 40136786)
45. Khanin, R., and Wit, E. (2006) How scale-free are biological networks. J. Comput. Biol. 13, 810-818 (Pubitemid 43801007)
46. Li, L., Alderson, D., Doyle, J. C., and Willinger, W. (2005) Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications. Internet Math. 2, 431-523
47. Tanaka, R., Yi, T. M., and Doyle, J. (2005) Some protein interaction data do not exhibit power law statistics. FEBS Lett. 579, 5140-5144 (Pubitemid 41318082)
48. Bollobas, B., and Riordan, O. (2003) Robustness and Vulnerability of Scale- Free Random Graphs. Internet Math. 1, 1-35
49. Wu, J., Tan, Y., Deng, H., and Zhu, D. (2008) Relationship between degreerank function and degree distribution of protein-protein interaction networks. Comput Biol. Chem. 32, 1-4
50. Han, J. D., Dupuy, D., Bertin, N., Cusick, M. E., and Vidal, M. (2005) Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol. 23, 839-844 (Pubitemid 43093127)
51. de Chassey, B., Meyniel-Schicklin, L., Aublin-Gex, A., Andre, P., and Lotteau, V. (2012) Genetic screens for the control of influenza virus replication: from meta-analysis to drug dicovery. Mol. Biosyst. 8, 1297-1303
52. Davey, N. E., Edwards, R. J., and Shields, D. C. (2010) Computational identification and analysis of protein short linear motifs. Front. Biosci. 15, 801-825
53. Neduva, V., and Russell, R. B. (2006) Peptides mediating interaction networks: new leads at last. Curr. Opin. Biotechnol. 17, 465-471 (Pubitemid 44442924)