Bridging proteomics and systems biology: What are the roads to be traveled?

Proteomics

Volumn 5, Issue 16, 2005, Pages 4123-4137

  Souchelnytskyi, Serhiy ^a  

^a LUDWIG INSTITUTE FOR CANCER RESEARCH   (Sweden)

Author keywords

Systems biology

Indexed keywords

PROTEOME;

BIOLOGY; INFORMATION PROCESSING; MATHEMATICS; MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEOMICS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REVIEW; SIGNAL TRANSDUCTION; STANDARDIZATION;

ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, BIOLOGICAL; PROTEOME; PROTEOMICS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 27744477157     PISSN: 16159853     EISSN: None     Source Type: Journal    
DOI: 10.1002/pmic.200500135     Document Type: Review

References (113)

1. Butcher, E. C., Berg, E. L., Kunkel, E. J., Nat. Biotechnol. 2004, 22, 1253-1259.
2. Kitano, H., Nat. Rev. 2004, 4, 227-235.
3. Papin, J. A., Hunter, T., Palsson, B. O., Subramaniam, S., Nat. Rev. Mol. Cell Biol. 2005, 6, 99-111.
4. Ideker, T., Lauffenburger, D., Trends Biotechnol. 2003, 21, 255-262.
5. de Hoog, C., Mann, M., Annu. Rev. Genomics Hum. Genet. 2004, 5, 267-293.
6. Görg, A., Weiss, W., Dunn, M. J., Proteomics 2004, 4, 3665-3685.
7. Aggarwal, K., Lee, K. H., Brief. Funct. Genomics Proteomics 2003, 2, 175-184.
8. Cho, K.-H., Wolkenhauer, O., Biochem. Soc. Trans. 2003, 31, 1503-1509.
9. Hucka, M., Finney, A., Sauro, H. M., Bolouri, H. et al., Bioinformatics 2003, 19, 524-531.
10. Yang, X.-J., Oncogene 2005, 24, 1653-1662.
11. Pawson, T., Cell 2004, 116, 191-203.
12. Heldin, C.-H., Purton, M., Signal transduction, Chapman and Hall, London 1996, pp. 1-365.
13. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J. et al., Nat. Biotechnol. 2004, 22, 177-183.
14. Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et al., Nat. Biotechnol. 2003, 21, 247-254.
15. Pedrioli, P. G. A., Eng, J. K., Hubley, R., Vogelzang, M. et al., Nat. Biotechnol. 2004, 22, 1459-1466.
16. Stanislaus, R., Jiang, L. H., Swartz, M., Arthur, J., Almeida, J. S., BMC Bioinformatics 2004, 5, 9: 1-7.
17. http://www.geneontology.org
18. Adam, G. C., Sorensen, E. J., Cravatt, B. F., Mol. Cell. Proteomics 2002, 1, 781-790.
19. Cutler, P., Proteomics 2003, 3, 3-18.
20. Oda, Y., Nagasu, T., Chait, B. T., Nat. Biotechnol. 2001, 19, 379-382.
21. Zhou, H., Watts, J. D., Aebersold, R., Nat. Biotechnol. 2001, 19, 375-378.
22. Vosseller, K., Hansen, K. C., Chalkley, R. J., Trinidad, J. C. et al., Proteomics 2005, 5, 388-398.
23. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Nat. Biotechnol. 1999, 17, 994-999.
24. Ong, S. E., Foster, L. J., Mann, M., Methods 2003, 29, 124-130.
25. Julka, S., Regnier, F., J. Proteome Res. 2004, 3, 350-363.
26. Schmidt, A., Kellermann, J., Lottspeich, F., Proteomics 2005, 5, 4-15.
27. Gevaert, K., Goethals, M., Martens, L., Van Damme, J. et al., Nat. Biothecnol. 2003, 21, 566-569.
28. Blagoev, B., Ong, S.-E., Kratchmarova, I., Mann, M., Nat. Biotechnol. 2004, 22, 1139-1145.
29. Reinders, J., Lewandowski, U., Moebius, J., Wagner, Y., Sickmann, A., Proteomics 2004, 4, 3786-3703.
30. Traxler, E., Bayer, E., Stöckl, J., Mohr, T. et al., Proteomics 2004, 4, 1314-1323.
31. Gerner, C., Vejda, S., Gelbmann, D., Bayer, E. et al., Mol. Cell. Proteomics 2002, 1, 528-537.
32. Greighton, T. E., Proteins: Structure and molecular properties, Freeman, New York 1993, pp. 78-102.
33. Pawson, T., Cell 2004, 116, 191-203.
34. Souchelnytskyi, S., Exp. Oncol. 2002, 24, 3-12.
35. Dubrovska, A., Souchelnytskyi, S., Proteomics 2005, in press.
36. Guy, G. R., Philip, R., Tan, Y. H., Electrophoresis 1994, 15, 417-440.
37. Stasyk, T., Dubrovska, A., Lomnytska, M., Yakymovych, I. et al., Mol. Biol. Cell 2005, DOI: 10.1091/mbc.E05-03-0257.
38. Knight, Z. A., Schilling, B., Row, R. H., Kenski, D. M. et al., Nat. Biotechnol. 2003, 21, 1047-1054.
39. Hirabayashi, J., Kasai, K.-I., J. Chromatogr. 2002, 721, 67-87.
40. Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C. et al., Nat. Biotechnol. 2004, 21, 921-926.
41. Vertegaal, A. C. O., Ogg, S. C., Jaffray, E., Rodriguez, M. S. et al., J. Biol. Chem. 2004, 279, 33791-33798.
42. Fu, M., Wang, C., Wang, J., Zafonte, B. T. et al., Cytokine Growth Factor Rev. 2002, 13, 259-276.
43. Umlauf, D., Goto, Y., Feil, R., Methods Mol Biol. 2004, 287, 99-120.
44. Ge, Y., Rajkumar, L., Guzman, R. C., Nandi, S. et al., Proteomics 2004, 4, 3464-3467.
45. Dudler, T., Gelb, M. H., J. Biol. Chem. 1996, 271, 11541-11547.
46. Fukuchi, M., Imamura, T., Chiba, T., Ebisawa, T. et al., Mol. Biol. Cell. 2001, 12, 1431-1443.
47. Jensen, L. J., Bork, P., DDT:Targets 2004, 3, 51-56.
48. Bader, G. D., Hogue, C. W. V., Nat. Biotechnol. 2002, 20, 991-997.
49. Gavin, A.-C., Bösche, M., Krause, R., Grandi, P. et al., Nature 2002, 415, 141-147.
50. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D. et al., Nature 2002, 415, 180-183.
51. Bouwmeester, T., Bauch, A., Ruffner, H., Angrand, P.-O. et al., Nat. Cell Biol. 2004, 6, 97-105.
52. Tran, H. T., Ulke, A., Morrice, N., Johannes, C. J., Moorhead, G. B. et al., Mol. Cell. Proteomics 2004, 3, 257-265.
53. Zhou, Y., Gu, G., Goodlett, D. R., Zhang, T. et al., J Biol. Chem. 2004, 279, 39155-39164.
54. Hasset, S., Eichner, A., Yakymovych, M., Hellman, U. et al., Proteomics 2004, 4, 1346-1358.
55. Grimsby, S., Jaensson, H., Dubrovska, A., Lomnytska, M. et al., FEBS Lett. 2004, 577, 93-100.
56. Phizicky, E. M., Fields, S., Microbiol. Rev. 1999, 59, 94-123.
57. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A. et al., Science 2003, 302, 1727-1736.
58. Li, S., Armstrong, C. M., Bertin, N., Ge, H. et al., Science 2003, 303, 540-543.
59. Colland, R, Jacq, X., Trouplin, V., Mougin, C. et al., Genome Res. 2004, 14, 1324-1332.
60. Elia, A. E. H., Cantley, L. C., Yaffe, M. B., Science 2003, 299, 1228-1231.
61. von Mering, C., Krause, R., Snel, B., Cornell, M. et al., Nature 2002, 417, 399-403.
62. Gagneur, J., Krause, R., Bouwmeester, T., Casari, G., Genome Biol. 2004, 5, R57.
63. Warnock, D. E., Fahy, E., Taylor, S. W., Mass Spectrom. Rev. 2004, 23, 259-280.
64. Skop, A. R., Liu, H., Yates, J. III, Meyer, B. J., Heald, R., Science 2004, 305, 61-66.
65. Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P. et al., Nature 2003, 426, 570-574.
66. Sickmann, A., Reinders, J., Wagner, Y., Joppich, C. et al., Proc. Natl. Acad. Sci. USA 2003, 100, 13207-13212.
67. Taylor, S. W., Fahy, E., Zhang, B., Glenn, G. M. et al., Nat. Biotechnol. 2003, 21, 281-286.
68. Mootha, V. K., Bunkenborg, J., Olsen, J., V., Hjerrild, M. et al., Cell 2003, 115, 629-640.
69. Brunei, S., Thibault, P., Gagnon, E., Kearney, P. et al., Trends Cell Biol. 2003, 13, 629-638.
70. Saghatelian, A., Jessani, N., Joseph, A., Humphrey, M., Cravatt, B. F., Proc. Natl. Acad. Sci. USA 2004, 101, 10000-10005.
71. Bredmeyer, A. J., Lweis, R. M., Malone, J. P., Davis, A. E. et al., Proc. Natl. Acad. Sci. USA 2004, 101, 11785-11790.
72. Besant, P. G., Lasker, M. V., Bui, C. D., Tan, E. et al., J. Proteome Res. 2004, 3, 120-125.
73. Liu, Y., Shah, K., Yang, F., Witucki, L., Shokat, K. M., Chem. Biol. 1998, 5, 91-101.
74. Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S. et al., Nature 2003, 425, 686-691.
75. Roix, J., Mistelli, T., Histochem. Cell. Biol. 2002, 118, 105-116.
76. Liebel, U., Starkuviene, V., Erfle, H., Simpson, J. C. et al., FEBS Lett. 2003, 554, 394-398.
77. Kumar, A., Agarwal, S., Heyman, J. A., Matson, S. et al., Genes Dev. 2002, 16, 707-719.
78. Mahajan, N. P., Linder, K., Berry, G., Gordon, G. W., et al., Nat. Biotechnol. 1998, 16, 547-552.
79. Hlavacek, W. S., Faeder, J. R., Blinov, M. L., Perelson, A. S., Goldstein, B., Biotechnol. Bioeng. 2003, 84, 783-794.
80. Batada, N. N., Shepp, L. A., Siegmund, D. O., Proc. Natl. Acad. Sci. USA 2004, 101, 6445-6449.
81. Peri, S., Navarro, D., Amanchy, R., Kristiansen, T. Z. et al., Genome Res. 2003, 13, 2363-2371.
82. Noble, D., BioEssays 2002, 24, 1155-1163.
83. Schoeberl, B., Eichler-Josson, C., Gilles, E. D., Muller, G., Nat. Biotechnol. 2002, 20, 370-375.
84. Ballif, B. A., Roux, P. P., Gerber, S. A., MacKeigan, J. P. et al., Proc. Natl. Acad. Sci. USA 2005, 102, 667-672.
85. Pomerening, J. R., Sontag, E. D., Ferrell, J. E., Nat. Cell Biol. 2003, 5, 346-351.
86. Soskic, V., Godovac, M., Poznanovic, S., Boehmer, F. D., Godovac-Zimmermann, J., Biochemistry 1999, 38, 1757-1764.
87. El Yazidi-Belkoura, I., Adriaenssens, E., Dolle, L., Descamps, S., Hondermarck, H., J. Biol. Chem. 2003, 278, 16952-16956.
88. Kanamoto, T., Hellman, U., Heldin, C.-H., Souchelnytskyi, S., EMBO J. 2002, 21, 1219-1230.
89. Bornheimer, S. J., Maurya, M. R., Farquhar, M. G., Subramaniam, S., Proc. Natl. Acad. Sci. USA 2004, 101, 15899-15904.
90. Ishii, N., Robert, M., Nakayama, Y., Kanai, A., Tomita, M. J., Biotechnology 2004, 113, 281-294.
91. Hasty, J., McMillen, D., Collins, J. J., Nature 2002, 420, 224-230.
92. Ferrigno, P., Silver, P., Oncogene 1999, 18, 6129-6134.
93. Kyoda, K. M., Muraki, M., Kitano, H., Pac. Symp. Biocomput. 2000, 317-328.
94. Vo, T. D., Greenberg, H. J., Palsson, B. O., J. Biol. Chem. 2004, 279, 39532-39540.
95. Behre, G., Reddy, V. A., Tenen, D. G., Hiddemann, W., Zada, A. A., Singh, S. M., Expert. Opin. Ther. Targets 2002, 6, 491-495.
96. Souchelnytskyi, S., J. Mammary Gland Biol. Neoplasia 2002, 7, 39-371.
97. Eungdamrong, N. J., lyengar, R., Biol. Cell 2004, 96, 355-362.
98. Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R. et al., Science 2001, 292, 929-933.
99. Van, W., Lee, H., Yi, E. C., Reiss, D. et al., Genome Biol. 2004, 5, R54.
100. Plavec, I., Sirenko, O., Privat, S., Wang, Y. et al., Proc. Natl. Acad. Sci. USA 2004, 101, 1223-1228.
101. Spirin, V., Mirny, L. A., Proc. Natl. Acad. Sci. USA 2003, 100, 12123-12128.
102. Kutalik, Z., Cho, K-H., Wolkenhauer, O., BioSystems 2004, 75, 43-45.
103. Cho, K.-H., Shin, S.-Y, Lee, H.-W., Wolkenhauer, O., Genome Res. 2003, 13, 2413-2422.
104. Amaral, L. A. N., Diaz-Guilera, A., Moreira, A. A., Goldberger, A. L., Lipsitz, L. A., Proc. Natl. Acad. Sci. USA 2004, 101, 15551-15555.
105. Kauffman, S., Peterson, C., Samuelsson, B., Troein, C., Proc. Natl. Acad. Sci. USA 2004, 101, 17102-17107.
106. Huang, S., Ingber, D. E., Exp. Cell Res. 2000, 261, 91-103.
107. Sachs, K., Gifford, D., Jaakkola, T., Sorger, P. Lauffenburger, D. A., Science's STKE 2002, http://stke.sciencemag.org/cgi/content/full/sigtrans;2002/ 148/pe38.
108. Angeli, D., Ferrell, J. E., Sontag, E. D., Proc. Natl. Acad. Sci. USA 2004, 101, 1822-1827.
109. Song, C., Havlin, S., Makse, H. A., Nature 2005, 433, 392-395.
110. Van der Greet, J., Stroobant, P., van der Heijden, R., Curr. Opin Chem. Biol. 2004, 8, 559-565.
111. Weston, A.D., Hood, L., J. Prot. Res. 2004, 3, 179-196.
112. Oksman-Caldentey, K-M., Inzé, D., Oresic, M., Proc. Natl. Acad. Sci. USA 2004, 101, 9949-9950.
113. Mayr, M., Mayr, U., Chung, Y.-L., Yin, X. et al., Proteomics 2004, 4, 3751-3761.