Genetic reconstruction of a functional transcriptional regulatory network (original) (raw)

References

  1. Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
    Article CAS Google Scholar
  2. Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004).
    Article CAS Google Scholar
  3. Sekinger, E.A. & Gross, D.S. Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105, 403–414 (2001).
    Article CAS Google Scholar
  4. Radonjic, M. et al. Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell 18, 171–183 (2005).
    Article CAS Google Scholar
  5. Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109–126 (2000).
    Article CAS Google Scholar
  6. Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28, 327–334 (2001).
    Article CAS Google Scholar
  7. Hahn, J.S., Hu, Z., Thiele, D.J. & Iyer, V.R. Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol. Cell. Biol. 24, 5249–5256 (2004).
    Article CAS Google Scholar
  8. Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001).
    Article CAS Google Scholar
  9. Van Driessche, N. et al. Epistasis analysis with global transcriptional phenotypes. Nat. Genet. 37, 471–477 (2005).
    Article CAS Google Scholar
  10. Yeang, C.H. et al. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 6, R62 (2005).
    Article Google Scholar
  11. Hartemink, A.J., Gifford, D.K., Jaakkola, T.S. & Young, R.A. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac. Symp. Biocomput. 422–433 (2001).
  12. Mnaimneh, S. et al. Exploration of essential gene functions via titratable promoter alleles. Cell 118, 31–44 (2004).
    Article CAS Google Scholar
  13. Zhu, J. & Zhang, M.Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15, 607–611 (1999).
    Article CAS Google Scholar
  14. Chiang, D.Y., Moses, A.M., Kellis, M., Lander, E.S. & Eisen, M.B. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol. 4, R43 (2003).
    Article Google Scholar
  15. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003).
    Article CAS Google Scholar
  16. 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. Nat. Biotechnol. 16, 939–945 (1998).
    Article CAS Google Scholar
  17. Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994).
    CAS PubMed Google Scholar
  18. Liu, X.S., Brutlag, D.L. & Liu, J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835–839 (2002).
    Article CAS Google Scholar
  19. Dilova, I., Aronova, S., Chen, J.C. & Powers, T. Tor signaling and nutrient-based signals converge on Mks1p phosphorylation to regulate expression of Rtg1.Rtg3p-dependent target genes. J. Biol. Chem. 279, 46527–46535 (2004).
    Article CAS Google Scholar
  20. Komeili, A., Wedaman, K.P., O'Shea, E.K. & Powers, T. Mechanism of metabolic control. Target of rapamycin signaling links nitrogen quality to the activity of the Rtg1 and Rtg3 transcription factors. J. Cell Biol. 151, 863–878 (2000).
    Article CAS Google Scholar
  21. Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34, 166–176 (2003).
    Article CAS Google Scholar
  22. Simon, I. et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697–708 (2001).
    Article CAS Google Scholar
  23. Rosenfeld, N. & Alon, U. Response delays and the structure of transcription networks. J. Mol. Biol. 329, 645–654 (2003).
    Article CAS Google Scholar
  24. Hall, D.A. et al. Regulation of gene expression by a metabolic enzyme. Science 306, 482–484 (2004).
    Article CAS Google Scholar
  25. Sopko, R. et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21, 319–330 (2006).
    Article CAS Google Scholar
  26. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999).
    Article CAS Google Scholar
  27. 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).
    Article CAS Google Scholar
  28. Killion, P.J., Sherlock, G. & Iyer, V.R. The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinformatics 4, 32 (2003).
    Article Google Scholar
  29. Eisen, M.B. & Brown, P.O. DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179–205 (1999).
    Article CAS Google Scholar

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