Conserved patterns of protein interaction in multiple species

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

Volumn 102, Issue 6, 2005, Pages 1974-1979

  Sharan, Roded ^a,d   Suthram, Silpa ^b   Kelley, Ryan M ^b   Kuhn, Tanja ^c   McCuine, Scott ^b   Uetz, Peter ^c   Sittler, Taylor ^b   Karp, Richard M ^a   Ideker, Trey ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^d TEL AVIV UNIVERSITY   (Israel)

Author keywords

Comparative analysis; Multiple alignment; Protein network; Yeast two hybrid

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CAENORHABDITIS ELEGANS; COMPARATIVE STUDY; DROSOPHILA MELANOGASTER; GENETIC CONSERVATION; GENOME; METAZOON; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; TWO HYBRID SYSTEM; YEAST;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS ELEGANS PROTEINS; DATABASES, NUCLEIC ACID; DROSOPHILA PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; TWO-HYBRID SYSTEM TECHNIQUES;

ARACHNIDA; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; HEXAPODA; MELANOGASTER; METAZOA; NEMATODA; SACCHAROMYCES CEREVISIAE;

EID: 13844314048     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0409522102     Document Type: Article

References (34)

1. Fields, S. & Song, O. (1989) Nature 340, 245-246.
2. Aebersold, R. & Mann, M. (2003) Nature 422, 198-207.
3. 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.
4. 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.
5. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. & Sakaki, Y. (2001) Proc. Natl. Acad. Sci. USA 98, 4569-4574.
6. 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.
7. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Crucial, C. M., et al. (2002) Nature 415, 141-147.
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. Samanta, M. P. & Liang, S. (2003) Proc. Natl. Acad. Sci. USA 100, 12579-12583.
11. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. & Bork, P. (2002) Nature 417, 399-403.
12. Matthews, L. R., Vaglio, P., Reboul, J., Ge, H., Davis, B. P., Garrels, J., Vincent, S. & Vidal, M. (2001) Genome Res. 11, 2120-2126.
13. Kelley, B. P., Sharan, R., Karp, R. M., Sittler, T., Root, D. E., Stockwell, B. R. & Ideker, T. (2003) Proc. Natl. Acad. Sci. USA 100, 11394-11399.
14. Sharan, R., Ideker, T., Kelley, B. P., Shamir, R. & Karp, R. M. (2004) in Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology-RECOMB, eds. Bourne, P. E. & Gusfield, D. (Am. Soc. Microbiol. Press, Washington, DC), pp. 282-289.
15. Dandekar, T., Schuster, S., Snel, B., Huynen, M. & Bork, P. (1999) Biochem. J. 343, 115-124.
16. Forst, C. V. & Schulten, K. (2001) J. Mol. Evol. 52, 471-489.
17. Ogata, H., Fujibuchi, W., Goto, S. & Kanehisa, M. (2000) Nucleic Acids Res. 28, 4021-4028.
18. Stuart, J. M., Segal, E., Koller, D. & Kim, S. K. (2003) Science 302, 249-255.
19. Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varki, A., Ravid, R., et al. (2002) Science 296, 340-343.
20. Bergmann, S., Ihmels, J. & Barkai, N. (2004) PLoS Biol. 2, E9.
21. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
22. Bader, J. S., Chaudhuri, A., Rothberg, J. M. & Chant, J. (2004) Nat. Biotechnol. 22, 78-85.
23. Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. M. & Eisenberg, D. (2002) Nucleic Acids Res. 30, 303-305.
24. Christie, K. R., Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., et al. (2004) Nucleic Acids Res. 32, D311-D314.
25. Harris, T. W., Chen, N., Cunningham, F., Tello-Ruiz, M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Chan, J., et al. (2004) Nucleic Acids Res. 32, D411-D417.
26. Flybase Consortium (2003) Nucleic Acids Res. 31, 172-175.
27. Mewes, H. W., Amid, C., Arnold, R., Frishman, D., Guldener, U., Mannhaupt, G., Munsterkotter, M., Pagel, P., Strack, N., Stumpflen, V., et al. (2004) Nucleic Acids Res. 32, D41-D44.
28. Xie, H., Wasserman, A., Levine, Z., Novik, A., Grebinskiy, V., Shoshan, A. & Mintz, L. (2002) Genome Res. 12, 785-794.
29. Yu, H., Luscombe, N. M., Lu, H. X., Zhu, X., Xia, Y., Han, J. D., Bertin, N., Chung, S., Vidal, M. & Gerstein, M. (2004) Genome Res. 14, 1107-1118.
30. Schmid, H. P., Pouch, M. N., Petit, F., Dadet, M. H., Badaoui, S., Boissonnet, G., Buri, J., Norris, V. & Briand, Y. (1995) Mol. Biol. Rep. 21, 43-47.
31. Gautier-Bert, K., Murol, B., Jarrousse, A. S., Ballut, L., Badaoui, S., Petit, F. & Schmid, H. P. (2003) Mol. Biol. Rep. 30, 1-7.
32. Yu, T. W. & Bargmann, C. I. (2001) Nat. Neurosci. 4, Suppl., 1169-1176.
33. Spira, M. E., Oren, R., Dormann, A., Ilouz, N. & Lev, S. (2001) Cell Mol. Neurobiol. 21, 591-604.
34. 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.