Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae

Proceedings of the National Academy of Sciences of the United States of America

Volumn 101, Issue 52, 2004, Pages 18006-18011

  Said, Maya R ^a   Begley, Thomas J ^b,c,d   Oppenheim, Alan V ^a   Lauffenburger, Douglas A ^b,c   Samson, Leona D ^b,c  

^a USA   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c Massachusetts Institute of Technology Cambridge   (United States)

^d STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

DNA damage; DNA repair; Graph theory; Signaling; Systems and computational biology

Indexed keywords

ARTICLE; CELL FUNCTION; COMPLEX FORMATION; DNA DAMAGE; DNA REPAIR; FUNGAL GENETICS; GENOME; GENOTYPE; GLOBAL NETWORK ANALYSIS; GRAPH THEORY; MODULATION; MOLECULAR BIOLOGY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN NETWORK; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS; THEORY; TOXICITY;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENOME, FUNGAL; MODELS, BIOLOGICAL; MODELS, THEORETICAL; PHENOTYPE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SOFTWARE;

SACCHAROMYCES CEREVISIAE;

EID: 11144234660     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0405996101     Document Type: Article

References (35)

1. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al. (2002) Nature 415, 180-183.
2. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) Nature 403, 623-627.
3. Tong, A. H., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Page, N., Robinson, M., Raghibizadeh, S., Hogue, C. W., Bussey, H., et al. (2001) Science 294, 2364-2368.
4. Tong, A. H., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., Brost, R. L., Chang, M., et al. (2004) Science 303, 808-813.
5. Fromont-Racine, M., Rain, J. C. & Legrain, P. (1997) Nat. Genet. 16, 277-282.
6. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. & Sakaki, Y. (2001) Proc. Natl. Acad. Sci. USA 98, 4569-4574.
7. Rain, J. C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schachter, V., et al. (2001) Nature 409, 211-215.
8. Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C. E., Godwin, B., Vitols, E., et al. (2003) Science 302, 1727-1736.
9. Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P. O., Han, J. D., Chesneau, A., Hao, T., et al. (2004) Science 303, 540-543.
10. Walhout, A. J., Sordella, R., Lu, X., Hartley, J. L., Temple, G. F., Brasch, M. A., Thierry-Mieg, N. & Vidal, M. (2000) Science 287, 116-122.
11. Achacoso, T. & Yamamoto, W. (1992) Neuroanatomy of C. elegans for Computation (CRC, Boca Raton, FL).
12. Watts, D. J. & Strogatz, S. H. (1998) Nature 393, 440-442.
13. Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. (2000) Nature 407, 651-654.
14. Wagner, A. & Fell, D. A. (2001) Proc. R. Soc. London Ser. B 268, 1803-1810.
15. Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. (2001) Nature 411, 41-42.
16. Maslov, S. & Sneppen, K. (2002) FEBS. Lett. 530, 255-256.
17. Maslov, S. & Sneppen, K. (2002) Science 296, 910-913.
18. Guelzim, N., Bottani, S., Bourgine, P. & Kepes, F. (2002) Nat. Genet. 31, 60-63.
19. Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) Science 298, 799-804.
20. Ren, B., Robert, F., Wyrick, J. J., Aparicio, O., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. (2000) Science 290, 2306-2309.
21. Barabasi, A.-L. & Oltvai, Z. N. (2004), Nat. Rev. Genet. 5, 101-113.
22. Dezso, Z., Oltvai, Z. N. & Barabasi, A. L. (2003) Genome. Res. 11, 2450-2454.
23. Han, J-D. J., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J. M., Cusiek, M. E., Roth, F. P. & Vidal, M. (2004) Nature 430, 88-93.
24. Begley, T. J., Rosenbach, A. S., Ideker, T. & Samson, L. D. (2002) Mol. Cancer Res. 1, 103-112.
25. Begley, T. J., Rosenbach, A. S., Ideker, T. & Samson, L. D. (2004) Mol. Cell., 16, 117-125.
26. Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. M. & Eisenberg, D. (2002) Nucleic. Acids Res. 30, 303-305.
27. Devore, J. L. (2004) Probability and Statistics (Brooks/Cole-Thomason, Belmont, CA), 6th Ed.
28. Spirin, V. & Mirny, L. A. (2003) Proc. Natl. Acad. Sci. USA 100, 12123-12128.
29. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B. & Ideker, T. (2003) Genome. Res. 13, 2498-2504.
30. Forster, J., Famili, I., Fu, P., Palsson, B. & Nielsen, J. (2003) Gen. Res. 13, 244-253.
31. Gavin, A.-C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A.-M., Cruciat, C.-M., et al. (2002) Nature 415, 141-147.
32. Deane, C. M., Salwinski, L., Xenarios, I. & Eisenberg, D. (2002). Mol. Cell. Proteomics 1, 349-356.
33. Jelinsky, S. A. & Samson, L. D. (1999) Proc. Natl. Acad. Sci. USA 96, 1486-1491.
34. Jelinsky, S. A., Estep, P., Church, G. M. & Samson, L. D. (2000) Mol. Cell. Biol. 20, 8157-8167.
35. Lauffenburger, D. A. (2000) Proc. Natl. Acad. Sci. USA 97, 5031-5033.