Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

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

Volumn 101, Issue 16, 2004, Pages 5934-5939

  Yeger Lotem, Esti ^a,b   Sattath, Shmuel ^a   Kashtan, Nadav ^c   Itzkovitz, Shalev ^c   Milo, Ron ^c   Pinter, Ron Y ^b   Alon, Uri ^c   Margalit, Hanah ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CONTROLLED STUDY; FEEDBACK SYSTEM; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION;

AMINO ACID MOTIFS; GENE EXPRESSION REGULATION; PROTEIN BINDING; PROTEINS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 1942469444     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0306752101     Document Type: Article

References (46)

1. Thieffry, D., Huerta, A. M., Perez-Rueda, E. & Collado-Vides, J. (1998) BioEssays 20, 433-440.
2. Ouzounis, C. A. & Karp, P. D. (2000) Genome Res. 10, 568-576.
3. Fell, D. A. & Wagner, A. (2000) Nat. Biotechnol. 18, 1121-1122.
4. Guelzim, N., Bottani, S., Bourgine, P. & Kepes, F. (2002) Nat. Genet. 31, 60-63.
5. 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.
6. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. & Sakaki, Y. (2001) Proc. Natl. Acad. Sci. USA 98, 4569-4574.
7. Iyer, V. R., Horak, C. E., Scafe, C. S., Botstein, D., Snyder, M. & Brown, P. O. (2001) Nature 409, 533-538.
8. Simon, I., Barnett, J., Hannett, N., Harbison, C. T., Rinaldi, N. J., Volkert, T. L., Wyrick, J. J., Zeitlinger, J., Gifford, D. K., Jaakkola, T. S. & Young, R. A. (2001) Cell 106, 697-708.
9. 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.
10. 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.
11. Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. (2002) Nat. Genet. 31, 64-68.
12. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. & Alon, U. (2002) Science 298, 824-827.
13. Rives, A. W. & Galitski, T. (2003) Proc. Natl. Acad. Sci. USA 100, 1128-1133.
14. Bu, D., Zhao, Y., Cai, L., Xue, H., Zhu, X., Lu, H., Zhang, J., Sun, S., Ling, L., Zhang, N., Li, G. & Chen, R. (2003) Nucleic Acids Res. 31, 2443-2450.
15. Spirin, V. & Mirny, L. A. (2003) Proc. Natl. Acad. Sci. USA 100, 12123-12128.
16. Wuchty, S., Oltvai, Z. N. & Barabasi, A. L. (2003) Nat. Genet. 35, 176-179.
17. Zhu, J. & Zhang, M. Q. (1999) Bioinformatics 15, 607-611.
18. Costanzo, M. C., Crawford, M. E., Hirschman, J. E., Kranz, J. E., Olsen, P., Robertson, L. S., Skrzypek, M. S., Braun, B. R., Hopkins, K. L., Kondu, P., et al. (2001) Nucleic Acids Res. 29, 75-79.
19. Xenarios, I., Fernandez, E., Salwinski, L., Duan, X. J., Thompson, M. J., Marcotte, E. M. & Eisenberg, D. (2001) Nucleic Acids Res. 29, 239-241.
20. Bader, G. D., Donaldson, I., Wolting, C., Ouellette, B. F., Pawson, T. & Hogue, C. W. (2001) Nucleic Acids Res. 29, 242-245.
21. Mewes, H. W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S. & Weil, B. (2002) Nucleic Acids Res. 30, 31-34.
22. Sprinzak, E., Sattath, S. & Margalit, H. (2003) J. Mol. Biol. 327, 919-923.
23. Yeger-Lotem, E. & Margalit, H. (2003) Nucleic Acids Res. 31, 6053-6061.
24. Newman, M. E., Strogatz, S. H. & Watts, D. J. (2001) Phys. Rev. E Stat Nonlin. Soft Matter Phys. 64, 026118.
25. Maslov, S. & Sneppen, K. (2002) Science 296, 910-913.
26. Lohr, D., Venkov, P. & Zlatanova, J. (1995) FASEB J. 9, 777-787.
27. Rosenfeld, N., Elowitz, M. B. & Alon, U. (2002) J. Mol. Biol. 323, 785-793.
28. Rosenfeld, N. & Alon, U. (2003) J. Mol. Biol. 329, 645-654.
29. Ferrell, J. E., Jr. (2002) Curr. Opin. Cell Biol. 14, 140-148.
30. Elowitz, M. B. & Leibler, S. (2000) Nature 403, 335-338.
31. Tyson, J. J., Chen, K. C. & Novak, B. (2003) Curr. Opin. Cell Biol. 15, 221-231.
32. Vogelstein, B., Lane, D. & Levine, A. J. (2000) Nature 408, 307-310.
33. Hoffmann, A., Levchenko, A., Scott, M. L. & Baltimore, D. (2002) Science 298, 1241-1245.
34. Santoro, M. G. (2000) Biochem. Pharmacol. 59, 55-63.
35. Straus, D., Walter, W. & Gross, C. A. (1990) Genes Dev. 4, 2202-2209.
36. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. & Barkai, N. (2002) Nat. Genet. 31, 370-377.
37. Laub, M. T., McAdams, H. H., Feldblyum, T., Fraser, C. M. & Shapiro, L. (2000) Science 290, 2144-2148.
38. Grigoriev, A. (2001) Nucleic Acids Res. 29, 3513-3519.
39. Kemmeren, P., van Berkum, N. L., Vilo, J., Bijma, T., Donders, R., Brazma, A. & Holstege, F. C. (2002) Mol. Cell 9, 1133-1143.
40. Mangan, S. & Alon, U. (2003) Proc. Natl. Acad. Sci. USA 100, 11980-11985.
41. Mangan, S., Zaslaver, A. & Alon, U. (2003) J. Mol. Biol. 334, 197-204.
42. Yuh, C. H., Bolouri, H. & Davidson, E. H. (1998) Science 279, 1896-1902.
43. Buchler, N. E., Gerland, U. & Hwa, T. (2003) Proc. Natl. Acad. Sci. USA 100, 5136-5141.
44. Setty, Y., Mayo, A. E., Surette, M. G. & Alon, U. (2003) Proc. Natl. Acad. Sci. USA 100, 7702-7707.
45. Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. (2001) Nature 411, 41-42.
46. Ronen, M., Rosenberg, R., Shraiman, B. I. & Alon, U. (2002) Proc. Natl. Acad. Sci. USA 99, 10555-10560.