Genomic analysis of regulatory network dynamics reveals large topological changes

Nature

Volumn 431, Issue 7006, 2004, Pages 308-312

  Luscombe, Nicholas M ^a   Babu, M Madan ^c   Yu, Haiyuan ^a   Snyder, Michael ^a   Teichmann, Sarah A ^c   Gerstein, Mark ^a,b  

^a YALE UNIVERSITY   (United States)

^b Yale University   (United States)

^c MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DATA ACQUISITION; LARGE SCALE SYSTEMS; MOLECULAR BIOLOGY; SIGNAL PROCESSING; STATISTICAL METHODS; TOPOLOGY;

BIOLOGICAL NETWORKS; GENE EXPRESSION; RANDOM SIMULATIONS; TRANSCRIPTION FACTORS;

GENE TRANSFER;

TRANSCRIPTION FACTOR;

BIOLOGY;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CELL CYCLE; ENVIRONMENTAL FACTOR; EUKARYOTE EVOLUTION; GENE EXPRESSION REGULATION; GENOME; LANGUAGE; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE; SANDY NETWORK; SIMULATION; SOCIAL INTERACTION; SPOROGENESIS; STATISTICAL ANALYSIS; TOPOGRAPHY; TRANSCRIPTION REGULATION;

ALGORITHMS; CELL CYCLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOMICS; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE; TRANSCRIPTION FACTORS;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 4644326931     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02782     Document Type: Article

References (28)

1. Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. The large-scale organization of metabolic networks. Nature 407, 651-654 (2000).
2. Guelzim, N., Bottani, S., Bourgine, P. & Kepes, F. Topological and causal structure of the yeast transcriptional regulatory network. Nature Genet. 31, 60-63 (2002).
3. Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824-827 (2002).
4. Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31, 64-68 (2002).
5. Oltvai, Z. N. & Barabasi, A. L. Systems biology. Life's complexity pyramid. Science 298, 763-764 (2002).
6. Barabasi, A. L. & Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nature Rev. Genet. 5, 101-113 (2004).
7. Milo, R. et al. Superfamilies of evolved and designed networks. Science 303, 1538-1542 (2004).
8. Teichmann, S. A. & Babu, M. M. Gene regulatory network growth by duplication. Nature Genet. 36, 492-496 (2004).
9. Svetlov, V. V. & Cooper, T. G. Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast 11, 1439-1484 (1995).
10. Horak, C. E. et al. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 16, 3017-3033 (2002).
11. Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
12. DeRisi, J. L., Iyer, V. R. & Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686 (1997).
13. Cho, R. J. et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2, 65-73 (1998).
14. Chu, S. et al The transcriptional program of sporulation in budding yeast. Science 282, 699-705 (1998).
15. Gasch, A. P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
16. Gasch, A. P. et al. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell 12, 2987-3003 (2001).
17. Odom, D. T. et al. Control of pancreas and liver gene expression by HNF transcription factors. Science 303, 1378-1381 (2004).
18. Zeitlinger, J. et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113, 395-404 (2003).
19. Watts, D. J. & Strogatz, S. H. Collective dynamics of 'small-world' networks. Nature 393, 440-442 (1998).
20. Wagner, A. & Fell, D. A. The small world inside large metabolic networks. Proc. R. Soc. Lond. B 268, 1803-1810 (2001).
21. Yu, H., Greenbaum, D., Xin Lu, H., Zhu, X. & Gerstein, M. Genomic analysis of essentiality within protein networks. Trends Genet. 20, 227-231 (2004).
22. Martinez-Antonio, A. & Collado-Vides, J. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6, 82-489 (2003).
23. Madan Babu, M. & Teichmann, S. A. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31, 1234-1244 (2003).
24. Pilpel, Y., Sudarsanam, P. & Church, G. M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genet. 29, 153-159 (2001).
25. Simon, I. et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697-708 (2001).
26. Ueda, H. R. et al. A transcription factor response element for gene expression during circadian night. Nature 418, 534-539 (2002).
27. Yu, H., Zhu, X., Greenbaum, D., Karro, J. & Gerstein, M. TopNet: a tool for comparing biological subnetworks, correlating protein properties with topological statistics. Nucleic Acids Res. 32, 328-337 (2004).
28. Christie, K. R. et al. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 32, D311-D314 (2004).