Understanding the dynamic behavior of genetic regulatory networks by functional decomposition

Current Genomics

Volumn 7, Issue 6, 2006, Pages 333-341

  Longabaugh, William ^a   Bolouri, Hamid ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

Genetic regulatory networks; Systems biology; Transcriptional regulation; Visualization

Indexed keywords

GALACTOSE; TRANSCRIPTION FACTOR;

AUTOREGULATION; CARBOHYDRATE METABOLISM; FEEDBACK SYSTEM; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE INTERACTION; GENE LOCATION; GENETIC REGULATION; HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN PROCESSING; REGULATORY SEQUENCE; REVIEW; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION;

EID: 33751423404     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920206778948718     Document Type: Review

References (50)

1. Davidson, E.H., Erwin, D.H., Gene regulatory networks and the evolution of animal body plans. Science 2006, 311: 796-800.
2. Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S.L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J.W., Cusick, M.E., Roth, F.P., Hill, D.E., Vidal, M., A map of the interactome network of the metazoan C. elegans. Science 2004, 303: 540-3.
3. Deplancke, B., Mukhopadhyay, A., Ao, W., Elewa, A.M., Grove, C.A., Martinez, N.J., Sequerra, R., Doucette-Stamm, L., Reece-Hoyes, J.S., Hope, I.A., Tissenbaum, H.A., Mango, S.E., Walhout, A.J., A gene-centered C. elegans protein-DNA interaction network. Cell 2006, 125: 1193-205.
4. Davidson, E.H. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. 2006: Elsevier.
5. Ihmels, J., Bergmann, S., Barkai, N., Defining transcription modules using large-scale gene expression data. Bioinformatics 2004, 20: 1993-2003.
6. Rives, A.W., Galitski, T., Modular organization of cellular networks. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:1128-33.
7. Shen-Orr, S.S., Milo, R., Mangan, S., Alon, U., Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 2002, 31: 64-8.
8. 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., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K., Young, R.A., Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298: 799-804.
9. Bolouri, H., Davidson, E.H., Modeling transcriptional regulatory networks. Bioessays 2002, 24: 1118-29.
10. Tyson, J.J., Chen, K.C., Novak, B., Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell. Biol. 2003, 15: 221-31.
11. Hwang, D., Rust, A.G., Ramsey, S., Smith, J.J., Leslie, D.M., Weston, A.D., de Atauri, P., Aitchison, J.D., Hood, L., Siegel, A.F., Bolouri, H., A data integration methodology for systems biology. Proc. Natl. Acad. Sci. U. S.A. 2005, 102: 17296-301.
12. Hwang, D., Smith, J.J., Leslie, D.M., Weston, A.D., Rust, A.G., Ramsey, S., de Atauri, P., Siegel, A.F., Bolouri, H., Aitchison, J.D., Hood, L., A data integration methodology for systems biology: experimental verification. Proc. Natl. Acad. Sci. U. S. A. 2005, 102: 17302-7.
13. Ideker, T., Thorsson, V., Ranish, J.A., Christmas, R., Buhler, J., Eng, J.K., Bumgarner, R., Goodlett, D.R., Aebersold, R., Hood, L., Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292: 929-34.
14. Acar, M., Becskei, A., van Oudenaarden, A., Enhancement of cellular memory by reducing stochastic transitions. Nature 2005, 435: 228-32.
15. de Atuari P, O.D., Ramsey S, Bolouri H., Evolution of design principles in biochemcial networks. IEE Syst. Biol. 2004, 1: 28-40.
16. Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., Guenther, M.G., Kumar, R.M., Murray, H.L., Jenner, R.G., Gifford, D.K., Melton, D.A., Jaenisch, R., Young, R.A., Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122: 947-56.
17. Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.B., Reynolds, D.B., Yoo, J., Jennings, E.G., Zeitlinger, J., Pokholok, D.K., Kellis, M., Rolfe, P.A., Takusagawa, K.T., Lander, E.S., Gifford, D.K., Fraenkel, E., Young, R.A., Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431: 99-104.
18. Imai, K.S., Levine, M., Satoh, N., Satou, Y., Regulatory blueprint for a chordate embryo. Science 2006, 312: 1183-7.
19. Stathopoulos, A., Levine, M., Genomic regulatory networks and animal development Dev. Cell 2005, 9: 449-62.
20. Davidson, E.H., Rast, J.P., Oliveri, P., Ransick A., Calestani, C., Yuh, C.H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C.T., Livi, C.B., Lee, P.Y., Revilla, R., Rust, A.G., Pan, Z., Schilstra, M.J., Clarke, P.J., Arnone, M.I., Rowen, L., Cameron, R.A., McClay, D.R., Hood, L., Bolouri, H., A genomic regulatory network for development Science 2002, 295: 1669-78.
21. Mangan, S., Itzkovitz, S., Zaslaver, A., Alon, U., The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J. Mol. Biol. 2006, 356: 1073-81.
22. Mangan, S., Alon, U., Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. U. S. A. 2003, 100: 11980-5.
23. Papatsenko, D., Levine, M., Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc. Natl. Acad. Sci. U. S. A. 2005, 102: 4966-71.
24. Servitja, J.M., Ferrer, J., Transcriptional Networks controlling pancreatic development and beta cell function. Diabetologica 2004, 47:597-613.
25. Gurdon, J.B., A community effect in animal development. Nature 1988, 336: 772-4.
26. Standley, H.J., Zom, A.M., Gurdon, J.B., eFGF and its mode of action in the community effect during Xenopus myogenesis. Development 2001, 128: 1347-57.
27. Weston, M.J.D., Kato, K. and, Gurdon, J.B., A community effect is required for amphibian notochord differentiation. Development Genes and Evolution 1994, 203: 250-3.
28. Ashburner, M., Puffs, genes and hormones revisited. Cell 1990, 61: 1-3.
29. Wolfgang, C.D., Liang, G., Okamoto, Y., Allen, A.E., Hai, T., Transcriptional autorepression of the stress-inducible gene ATF3. J. Biol. Chem. 2000, 275:16865-70.
30. Rosenfeld, N., Elowitz, M.B., Alon, U., Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 2002, 323: 785-93.
31. Koide, T., Hayata, T., Cho, K.W., Xenopus as a model system to study transcriptional regulatory networks. Proc. Natl. Acad. Sci. U. S. A. 2005, 102: 4943-8.
32. Hirata, H., Yoshiura, S., Ohtsuka, T., Bessho, Y., Harada, T., Yoshikawa, K., Kageyama, R., Oscillatory expression of the bHLH factor Hes 1 regulated by a negative feedback loop. Science 2002, 298:840-3.
33. Monk, N.A., Oscillatory expression of Hes1, p53 and NF-kappaB driven by transcriptional time delays. Curr. Biol. 2003, 13: 1409-13.
34. Alexandre, C., Vincent, J.P., Requirements for transcriptional repression and activation by Engrailed in Drosophila embryos. Development 2003, 130: 729-39.
35. Artavanis-Tsakonas, S., Rand, M.D., Lake, R.J., Notch signaling: cell fate control and signal integration in development Science 1999, 284: 770-6.
36. Jensen, J., Gene regulatory factors in pancreatic development Dev. Dyn. 2004, 229: 176-200.
37. Dekel, E., Mangan, S., Alon, U., Environmental selection of the feed-forward loop circuit in gene-regulation networks. Phys. Biol. 2005, 2:81-8.
38. Oliveri, P., Carrick, D.M., Davidson, E.H., A regulatory gene network that directs micromere specification in the sea urchin embryo. Dev. Biol. 2002, 246: 209-28.
39. Oliveri, P., Davidson, E.H., McClay, D.R., Activation of pmar1 controls specification of micromeres in the sea urchin embryo. Dev. Biol. 2003, 258: 32-43.
40. Hooshangi, S., Thiberge, S., Weiss, R., Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. U. S. A. 2005, 102: 3581-6.
41. Barolo, S., Posakony, J.W., Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling. Genes Dev. 2002, 16:1167-81.
42. Morel, V., Schweisguth, F., Repression by suppressor of hairless and activation by Notch are required to define a single row of single-minded expressing cells in the Drosophila embryo. Genes Dev. 2000, 14: 377-88.
43. Daniels, D.L., Weis, W.I., Beta-catenin directly displaces Groucho/TLE repressors from Tcf/Lef in Wnt-mediated transcription activation. Nat. Struct. Mol. Biol. 2005, 12: 364-71.
44. Istrail, S., Davidson, E.H., Logic functions of the genomic cis-regulatory code. Proc. Natl. Acad. Sci. U. S. A. 2005, 102: 4954-9.
45. Gilchrist, M., Thorsson, V., Li, B., Rust, A.G., Korb, M., Kennedy, K., Hai, T., Bolouri, H., Aderem, A., Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 2006, 441: 173-8.
46. Guet, C.C., Elowitz, M.B., Hsing, W., Leibler, S., Combinatorial synthesis of genetic networks. Science 2002, 296: 1466-70.
47. Morohashi, M., Winn, A.E., Borisuk, M.T., Bolouri, H., Doyle, J., Kitano, H., Robustness as a measure of plausibility in models of biochemical networks. J. Theor. Biol. 2002, 216: 19-30.
48. Cherry, J.L., Adler, F.R., How to make a biological switch. J. Theor. Biol. 2000, 203: 117-33.
49. Davidson, E.H., Rast, J.P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C.H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C.T., Livi, C.B., Lee, P.Y., Revilla, R., Schilstra, M.J., Clarke, P.J., Rust, A.G., Pan, Z., Arnone, M.I., Rowen, L., Cameron, R.A., McClay, D.R., Hood, L., Bolouri, H., A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev. Biol. 2002, 246: 162-90.
50. Longabaugh, W.J.R., Davidson, E.H., Bolouri, H., Computational representation of developmental genetic regulatory networks. Dev. Biol. 2005, 283: 1-16.