Systematic determination of genetic network architecture

Nature Genetics - Tập 22 Số 3 - Trang 281-285 - 1999
Saeed Tavazoie1, Jason D. Hughes1, Michael J. Campbell2, Raymond J. Cho3, George M. Church1
1Department of Genetics, Harvard Medical School, 200 Longwood Ave, Boston, 02115, Massachusetts, USA
2Molecular Applications Group, 607 Hansen Way, Building One, Palo Alto, 94303-1110, California, USA
3Department of Genetics, B400 Beckman Center, 279 Campus Drive

Tóm tắt

Từ khóa


Tài liệu tham khảo

Velculescu, V.E. et al. Characterization of the yeast transcriptome. Cell 88, 243–251 ( 1997).

Lockhart, D.J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675– 1680 (1996).

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).

Weinstein, J.N. et al. An information-intensive approach to the molecular pharmacology of cancer. Science 275, 343– 349 (1997).

Wen, X. et al. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl Acad. Sci. USA 95, 334–339 (1998).

Tavazoie, S. & Church, G.M. Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli. Nature Biotechnol. 16, 566– 571 (1998).

Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863– 14868 (1998).

Spellman, P.T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiase by microarray hybridization. Mol. Biol. Cell 9, 3273– 3297 (1998).

Holstege, F.C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717–728 (1998).

Tamayo, P. et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA 96, 2907– 2912 (1999).

Cho, R.J. et al. A genome wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2, 65–73 (1998).

Wodicka, L., Dong, H., Mittmann, M., Ho, M.H. & Lockhart, D.J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnol. 15, 1359 –1366 (1997).

Everitt, B. Cluster Analysis 122 (Heinemann, London, 1974).

Hartigan, J.A. Clustering Algorithms 351 (Wiley, New York, 1975).

Mewes, H.W. et al. Overview of the yeast genome. Nature 387, 7–65 (1997).

Roth, F.P., Hughes, J.D., Estep, P.W. & Church, G.M. Finding DNA-regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnol. 16, 949–945 (1998).

Schneider, T.D. & Stephens, R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097–6100 (1990).

Berg, O.G. & von Hippel, P.H. Selection of DNA-binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193, 723–750 ( 1987).

Koch, C. & Nasmyth, K. Cell cycle regulated transcription in yeast. Curr. Opin. Cell Biol. 6, 451– 459 (1994).

McInerny, C.J., Partridge, J.F., Mikesell, G.E., Creemer, D.P. & Breeden, L.L. A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription. Genes Dev. 11, 1277–1288 (1997).

Kuo, M. & Grayhack, E. A library of yeast genomic MCM1 binding sites contains genes involved in cell cycle control, cell wall and membrane structure, and metabolism. Mol. Cell. Biol. 14, 348–359 (1994).

Planta, R.J., Goncalves, M. & Mager, W.H. Global regulators of ribosome biosynthesis in yeast. Biochem. Cell Biol. 73, 825– 834 (1995).

Moskovina, E. et al. A search in the genome of Saccharomyces cerevisiae for genes regulated via stress response elements. Yeast 14, 1041–1050 (1998).

Thomas, D. & Surdin-Kerjan, Y. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 61, 503–532 ( 1997).