Targeting the human cancer pathway protein interaction network by structural genomics

Molecular and Cellular Proteomics

Volumn 7, Issue 10, 2008, Pages 2048-2060

  Huang, Yuanpang Janet ^a   Hang, Dehua ^a   Lu, Long Jason ^b,e   Tong, Liang ^c   Gerstein, Mark B ^b,d   Montelione, Gaetano T ^a  

^a RUTGERS UNIVERSITY   (United States)

^b YALE UNIVERSITY   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

^d Yale University   (United States)

^e CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

ACCESS TO INFORMATION; ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CANCER RESEARCH; COMPUTER NETWORK; HUMAN; HUMAN CANCER PATHWAY PROTEIN INTERACTION NETWORK DATABASE; INFORMATION RETRIEVAL; PRIORITY JOURNAL; PROCESS DESIGN; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; RELIABILITY; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

GENOMICS; HUMANS; NEOPLASM PROTEINS; NEOPLASMS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; REPRODUCIBILITY OF RESULTS;

EID: 55049132861     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700550-MCP200     Document Type: Article

References (85)

1. Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., and Stratton, M. R. (2004) A census of human cancer genes. Nat. Rev. Cancer 4, 177-183
2. Vogelstein, B., and Kinzier, K. W. (2004) Cancer genes and the pathways they control. Nat. Med. 10, 789-799
3. Greenman, C., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C., Edkins, S., O'Meara, S., Vastrik, I., Schmidt, E. E., Avis, T., Barthorpe, S., Bhamra, G., Buck, G., Choudhury, B., Clements, J., Cole, J., Dicks, E., Forbes, S., Gray, K., Halliday, K., Harrison, R., Hills, K., Hinton, J., Jenkinson, A., Jones, D., Menzies, A., Mironenko, T., Perry, J., Raine, K., Richardson, D., Shepherd, R., Small, A., Tofts, C., Varian, J., Webb, T., West, S., Widaa, S., Yates, A., Cahill, D. P., Louis, D. N., Goldstraw, P., Nicholson, A. G., Brasseur, F., Looijenga, L., Weber, B. L., Chiew, Y. E., DeFazio, A., Greaves, M. F., Green, A. R., Campbell, P., Birney, E., Easton, D. F., Chenevix-Trench, G., Tan, M. H., Khoo, S. K., Teh, B. T., Yuen, S. T., Leung, S. Y., Wooster, R., Futreal, P. A., and Stratton, M. R. (2007) Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158
4. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921
5. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., Gocayne, J. D., Amanatides, P., Bellew, R. M., Huson, D. H., Wortman, J. R., et al. (2001) The sequence of the human genome. Science 291, 1304-1351
6. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931-945
7. Liang, P., and Pardee, A. B. (2003) Analysing differential gene expression in cancer. Nat. Rev. Cancer 3, 869-876
8. Wulfkuhle, J., Espina, V., Liotta, L., and Petricoin, E. (2004) Genomic and proteomic technologies for individualisation and improvement of cancer treatment. Eur. J. Cancer 40, 2623-2632
9. Strausberg, R. L., Simpson, A. J., Old, L. J., and Riggins, G. J. (2004) Oncogenomics and the development of new cancer therapies. Nature 429, 469-474
10. Hornberg, J. J., Bruggeman, F. J., Westerhoff, H. V., and Lankelma, J. (2006) Cancer a systems biology disease. Biosystems 83, 81-90
11. Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya, M. A., Zhao, Z., Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, M., Choudhury, D. R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S. K., Madavan, V., Joseph, A., Wong, G. W., Schiemann, W. P., Constantinescu, S. N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G. C., Dang, C. V., Garcia, J. G., Pevsner, J., Jensen, O. N., Roepstorff, P., Deshpande, K. S., Chinnaiyan, A. M., Hamosh, A., Chakravarti, A., and Pandey, A. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 13, 2363-2371
12. 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
13. 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
14. Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G. R., Wu, G. R., Matthews, L., Lewis, S., Birney, E., and Stein, L. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33, D428-D432
15. Bader, G. D., Cary, M. P., and Sander, C. (2006) Pathguide: a pathway resource list. Nucleic Acids Res. 34, D504-D506
16. Cary, M. P., Bader, G. D., and Sander, C. (2005) Pathway information for systems biology. FEBS Lett. 579, 1815-1820
17. Lu, L J., Sboner, A., Huang, Y. J., Lu, H. X., Gianoulis, T. A., Yip, K. Y., Kim, P. M., Montelione, G. T., and Gerstein, M. B. (2007) Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem. Sci. 32, 320-331
18. Holm, L., and Sander, C. (1996) Mapping the protein universe. Science 273, 595-603
19. Shindyalov, I. N., and Bourne, P. E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11, 739-747
20. Yang, A. S., and Honig, B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J. Mol. Biol. 301, 665-678
21. Harris, T. (2000) Genetics, genomics, and drug discovery. Med. Res. Rev. 20, 203-211
22. Weng, Z., and DeLisi, C. (2002) Protein therapeutics: promises and challenges for the 21st century. Trends Biotechnol. 20, 29-35
23. Chandonia, J. M., and Brenner, S. E. (2006) The impact of structural genomics: expectations and outcomes. Science 311, 347-351
24. Brenner, S. E. (2001) A tour of structural genomics. Nat. Rev. Genet. 2, 801-809
25. Burley, S. K., and Bonanno, J. B. (2002) Structural genomics of proteins from conserved biochemical pathways and processes. Curr. Opin. Struct. Biol. 12, 383-391
26. Mueller, L, and Montelione, G. T. (2002) Structural genomics in pharmaceutical design. J. Struct. Funct. Genomics 2, 67-70
27. Xie, L., and Bourne, P. E. (2005) Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput. Biol. 1, e31
28. Bravo, J., and Aloy, P. (2006) Target selection for complex structural genomics. Curr. Opin. Struct Biol. 16, 385-392
29. Strong, M., Sawaya, M. R., Wang, S., Phillips, M., Cascio, D., and Eisenberg, D. (2006) Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Myoobacterium tuberculosis. Proc. Natl. Acad. Sci. U. S. A. 103, 8060-8065
30. Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Bimey, E., and Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4,1 985-1988
31. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., and Apweiler, R. (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32, D262-D266
32. Bendtsen, J. D., Nielsen, H., von Heijne, G., and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795
33. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J. Mol. Biol. 305, 567-580
34. Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L., Studholme, D. J., Yeats, C., and Eddy, S. R. (2004) The Pfam protein families database. Nucleic Acids Res. 32, D138-D141
35. Finn, R. D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., Eddy, S. R., Sonnhammer, E. L., and Bateman, A. (2006) Pfam: clans, web tools and services. Nucleic Acids Res. 34, D247-D251
36. Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting coiled coils from protein sequences. Science 252, 1162-1164
37. Wootton, J. C., and Federhen, S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266, 554-571
38. Uversky, V. N., Gillespie, J. R., and Fink, A. L. (2000) Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 41, 415-427
39. de Nooy, W., Mrvar, A., and Batagelj, V. (2005) Exploratory Social Network Analysis with Pajek, Cambridge University Press, Cambridge, UK
40. Dalgaard, P. (2002) Introductory Statistics with R, Springer, New York
41. Pieper, U., Eswar, N., Davis, F. P., Braberg, H., Madhusudhan, M. S., Rossi, A., Marti-Renom, M., Karchin, R., Webb, B. M., Eramian, D., Shen, M. Y., Kelly, L., Melo, F., and Sali, A. (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34, D291-D295
42. Bhattacharya, A., Wunderlich, Z., Monleon, D., Tejero, R., and Montelione, G. T. (2008) Assessing model accuracy using the homology modeling automatically (HOMA) software. Proteins 70, 105-118
43. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66, 778-795
44. Sippl, M. J. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355-362
45. Luthy, R., Bowie, J. U., and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profiles. Nature 356, 83-85
46. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thomton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
47. Lovell, S. C., Davis, I. W., Arendall, W. B., III, de Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S., and Richardson, D. C. (2003) Structure validation by Cα geometry: φ,ψ and Cβ deviation. Proteins 50, 437-450
48. Wittig, U., and De Beuckelaer, A. (2001) Analysis and comparison of metabolic pathway databases. Brief. Bioinform. 2, 126-142
49. Ding, C., He, X., Meraz, R. F., and Holbrook, S. R. (2004) A unified representation of multiprotein complex data for modeling interaction networks. Proteins 57, 99-108
50. Ramadan, E., Tarafdar, A., and Pothen, A. (2004) A hypergraph model for the yeast complex network, in the 18th International Parallel and Distributed Processing Symposium, page 189, Santa Fe, New Mexico, April 26-30, 2004
51. Barabasi, A. L., and Oltvai, Z. N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5,1 01-113
52. Yook, S. H., Oltvai, Z. N., and Barabasi, A. L. (2004) Functional and topological characterization of protein interaction networks. Proteomics 4, 928-942
53. Barrios-Rodiles, M., Brown, K. R., Ozdamar, B., Bose, R., Liu, Z., Donovan, R. S., Shinjo, F., Liu, Y., Dembowy, J., Taylor, I. W., Luga, V., Przulj, N., Robinson, M., Suzuki, H., Hayashizaki, Y., Jurisica, I., and Wrana, J. L. (2005) High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307, 1621-1625
54. Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178
55. Stelzi, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F. H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksoz, E., Droege, A., Krobitsch, S., Kom, B., Birchmeier, W., Lehrach, H., and Wanker, E. E. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957-968
56. Lim, J., Hao, T., Shaw, C., Patel, A. J., Szabo, G., Rual, J. F., Fisk, C. J., Li, N., Smolyar, A., Hill, D. E., Barabasi, A. L., Vidal, M., and Zoghbi, H. Y. (2006) A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125, 801-814
57. Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., and Barabasi, A. L. (2002) Hierarchical organization of modularity in metabolic networks. Science 297, 1551-1555
58. 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
59. Jeong, H., Mason, S. P., Barabasi, A. L., and Oltvai, Z. N. (2001) Lethality and centrality in protein networks. Nature 411, 41-42
60. Holme, P., Kim, B. J., Yoon, C. N., and Han, S. K. (2002) Attack vulnerability of complex networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65, 056109
61. Hahn, M. W., and Kem, A. D. (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol. Biol. Evol. 22, 803-806
62. Joy, M. P., Brock, A., Ingber, D. E., and Huang, S. (2005) High-betweenness proteins in the yeast protein interaction network. J. Biomed. Biotechnol. 2005, 96-103
63. Yu, H., Kim, P. M., Sprecher, E., Trifonov, V., and Gerstein, M. (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput. Biol. 3, e59
64. Wang, G., Bhalla, U. S., and Iyengar, R. (1999) Complexity in biological signaling systems. Science 284, 92-96
65. Marti-Renom, M. A., Stuart, A. C., Fiser, A., Sanchez, R., Melo, F., and Sali, A. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325
66. Baker, D., and Sali, A. (2001) Protein structure prediction and structural genomics. Science 294, 93-96
67. Erlandsen, H., Abola, E. E., and Stevens, R. C. (2000) Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites. Curr. Opin. Struct. Biol. 10, 719-730
68. Guigo, R., Flicek, P., Abril, J. F., Raymond, A., Lagarde, J., Denoeud, F., Antonarakis, S., Ashburner, M., Bajic, V. B., Bimey, E., Castelo, R., Eyras, E., Ucla, C., Gingeras, T. R., Harrow, J., Hubbard, T., Lewis, S. E., and Reese, M. G. (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 7, Suppl. 1, S21-S31
69. Wu, C. H., Apweiler, R., Bairoch, A., Natale, D. A., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Mazumder, R., O'Donovan, C., Redaschi, N., and Suzek, B. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34, D187-D191
70. Iakoucheva, L. M., Brown, C. J., Lawson, J. D., Obradovic, Z., and Dunker, A. K. (2002) Intrinsic disorder in cell-signaling and cancer-associated proteins. J. Mol. Biol. 323, 573-584
71. Oldfield, C. J., Ulrich, E. L., Cheng, Y., Dunker, A. K., and Markley, J. L. (2005) Addressing the intrinsic disorder bottleneck in structural proteomics. Proteins 59, 444-453
72. Wright, P. E., and Dyson, H. J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293, 321-331
73. Dunker, A. K., Brown, C. J., Lawson, J. D., Iakoucheva, L. M., and Obradovic, Z. (2002) Intrinsic disorder and protein function. Biochemistry 41, 6573-6582
74. Dyson, H. J., and Wright, P. E. (2002) Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 12, 54-60
75. Tompa, P. (2006) The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett. 579, 3346-3354
76. Liu, J., Hegyi, H., Acton, T. B., Montelione, G. T., and Rost, B. (2004) Automatic target selection for structural genomics on eukaryotes. Proteins 56, 188-200
77. Chandonia, J. M., and Brenner, S. E. (2005) Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 58, 166-179
78. Kim, S. H. (2000) Structural genomics of microbes: an objective. Curr. Opin. Struct. Biol. 10, 380-383
79. Goulding, C. W., Apostol, M., Anderson, D. H., Gill, H. S., Smith, C. V., Kuo, M. R., Yang, J. K., Waldo, G. S., Suh, S. W., Chauhan, R., Kale, A., Bachhawat, N., Mande, S. C., Johnston, J. M., Lott, J. S., Baker, E. N., Arcus, V. L., Leys, D., McLean, K. J., Munro, A. W., Berendzen, J., Sharma, V., Park, M. S., Eisenberg, D., Sacchettini, J., Alber, T., Rupp, B., Jacobs, W., Jr., and Terwilliger, T. C. (2002) The TB structural genomics consortium: providing a structural foundation for drug discovery. Curr. Drug Targets Infect. Disord. 2, 121-141
80. Matte, A., Sivaraman, J., Ekiel, I., Gehring, K., Jia, Z., and Cygler, M. (2003) Contribution of structural genomics to understanding the biology of Escherichia coli. J. Bacteriol. 185, 3994-4002
81. Brown, K. R., and Jurisica, I. (2005) Online predicted human interaction database. Bioinformatics 21, 2076-2082
82. Rhodes, D. R., Tomlins, S. A., Varambally, S., Mahavisno, V., Barrette, T., Kalyana-Sundaram, S., Ghosh, D., Pandey, A., and Chinnaiyan, A. M. (2005) Probabilistic model of the human protein-protein interaction network. Nat. Biotechnol. 23, 951-959
83. O'Donovan, C., Martin, M. J., Gattiker, A., Gasteiger, E., Bairoch, A., and Apweiler, R. (2002) High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief. Bioinform. 3, 275-284
84. Tolliday, N., Clemons, P. A., Ferraiolo, P., Koehler, A. N., Lewis, T. A., LI, X., Schreiber, S. L., Gerhard, D. S., and Eliasof, S. (20M) Small molecules, big players: the National Cancer Institute's Initiative for Chemical Genetics. Cancer Res. 66, 8935-8942
85. Spring, D. R. (2005) Chemical genetics to chemical genomics: small molecules offer big insights. Chem. Soc. Rev. 34, 472-482