Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries

DNA Research

Volumn 10, Issue 1, 2003, Pages 1-8

  Aburatani, Sachiyo ^a   Tashiro, Kosuke ^a,b   Savoie, Christopher J ^b   Nishizawa, Mayumi ^a   Hayashi, Kaori ^a   Ito, Yuzuru ^a   Muta, Shigeru ^a   Yamamoto, Kiyoshi ^a   Ogawa, Miki ^a   Enomoto, Akiko ^a   Masaki, Momoka ^a   Watanabe, Shouji ^c   Maki, Yukihiro ^c   Takahashi, Yoriko ^c   Eguchi, Yukihiro ^c   Sakaki, Yoshiyuki ^d   Kuhara, Satoru ^a,b  

^a KYUSHU UNIVERSITY   (Japan)

^b Gene Networks Inc   (United States)

^c Mitsui Knowledge Industry Co   (Japan)

^d RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

Disruptant; Expression data; Gene regulatory network; MET28 regulation

Indexed keywords

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BINDING SITE; CELL DIVISION; CELL FUNCTION; DNA REPAIR; GENE; GENE CONTROL; GENE FUNCTION; GENE MET28; GENE UME6; GENOME; MOLECULAR MODEL; NONHUMAN; REGULATORY MECHANISM; RELIABILITY; TRANSCRIPTION REGULATION;

ALGORITHMS; GENES, REGULATOR; GENOMIC LIBRARY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC;

EID: 0037254813     PISSN: 13402838     EISSN: None     Source Type: Journal    
DOI: 10.1093/dnares/10.1.1     Document Type: Article

References (26)

1. Pilpel, Y., Sudarsanam, P., and Church, G. M. 2001, Identifying regulatory networks by combinatorial analysis of promoter elements, Nature Genetics, 29, 153-159.
2. Friedman, N., Linial, M., Nachman, I., and Pe'er, D. 2000, Using Bayesian Networks to Analyze Expression Data, J. Comput Biol., 7, 601-620.
3. Somogyi, R. and Sniegoski, C. A. 1996, Modeling the complexity of genetic networks: Understanding multigene and pleiotropic regulation, Complexity, 1, 45-63.
4. Spellman, P. T., Sherlock, G., Zhang, M. Q. et al. 1998, Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization, Mol. Cell Biol., 9, 3273-3297.
5. Gasch, A. P., Spellman, P. T., Kao, C. M. et al. 1997, Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes, Mol. Cell Biol., 17, 2099-2106.
6. Akutsu, T., Miyano, S., and Kuhara, S. 2000, Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function, J. Comp. Biol., 7, 331-343.
7. Akutsu, T., Miyano, S., and Kuhara, S. 2000, Inferring qualitative relations in genetic networks and metabolic pathways, Bioinformatics; 16, 727-734.
8. Brown, M. P., Grundy, W. N., Lin, D. et al. 2000, Knowledge-based analysis of microarray gene expression data by using support vector machines, Proc. Natl. Acad. Sci. USA, 97, 262-267.
9. Ideker, T., Thorsson, V., Ranish, J. A. et al. 2001, Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network, Science, 292, 929-934.
10. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. 1995, Quantitative monitoring of gene expression patterns with a complementary DNA microarray, Science, 270, 467-470.
11. Shoudan, L. 1998, REVEAL, a general reverse engineering algorithm for inference of genetic network architectures, Pac. Sym. Biol., 3, 18-29.
12. Morgan, B. A., Bouquin, N., Merrill, G. F., and Johnston, L. H. 19957 A yeast transcription factor bypassing the requirement for SBF and DSC1/MBF in budding yeast has homology to bacterial signal transduction proteins, EMBO J., 14, 5679-5689.
13. Lorenz, M. C. and Heitman, J. 1998, Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains, Genetics, 150, 1443-1457.
14. Aguilera, A., Chavez, S., and Malagon, F. 2000, Mitotic recombination in yeast: elements controlling its incidence, Yeast, 16, 731-754.
15. Dasika, G. K., Lin, S. C., Zhao, S., Sung, P., Tomkinson, A., and Lee, E. Y. 1999, DNA damage-induced cell cycle checkpoints and DNA strand break repair in development and tumorigenesis, Oncogene, 18, 7883-7899.
16. Miura, F., Yada, T., Nakai, K., Sakaki, Y., and Ito, T. 2001, Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast, FEBS Lett., 505, 103-108.
17. Hiesinger, M., Roth, S., Meissner, E., and Schuller, H. J. 2001, Contribution of Cat8 and Sip4 to the transcriptional activation of yeast gluconeogenic genes by carbon source-responsive elements, Curr. Genet., 39, 68-76.
18. Carman, G. M. and Henry, S. A. 1999, Phospholipid biosynthesis in the yeast Saccharomyces cerevisiae and interrelationship with other metabolic processes, Prog. Lipid Res., 38, 361-399.
19. Jiang, R. and Carlson, M. 1997, The Snf1 protein kinase and its activating subunit, Snf4, interact with distinct domains of the Sip1/Sip2/Ga183 component in the kinase complex, Mol. Cell Biol., 17, 2099-2106.
20. Kuras, L., Cherest, H., Surdin-Kerjan, Y., and Thomas, D. 1996, A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediate the transcription activation of yeast sulfur metabolism, EMBO J., 15, 2519-2529.
21. Newman, J. R. S., Wolf, E., and Kim, P. S. 2000, A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae, Proc. Natl. Acad. Sci USA., 97, 13203-13208.
22. Bowdish, K. S., Yuan, H. E., and Mitchell, A. P. 1995, Positive control of yeast meiotic genes by the negative regulator UME6, Mol. Cell Biol., 15, 2955-2961.
23. Rubin-Bejerano, I., Mandel, S., Robzyk, K., and Kassir, Y. 1996, Induction of meiosis in Saccharomyces cerevisiae depends on conversion of the transcriptional repressor Ume6 to a positive regulator by its regulated association with the transcriptional activator Ime1, Mol. Cell Biol., 16, 2518-2526.
24. Bailey, T. L. and Elkan, C. 1994, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press Menlo Park, California, 28-36.
25. Luche, R. M., Sumrada, R., and Cooper, T. G., 1990, A cis-acting element present in multiple genes serves as a repressor protein binding site for the yeast CAR1 gene, Mol. Cell Biol., 10, 3884-3895.
26. Messenguy, F., Vierendeels, F., Scherens, B., and Dubois, E. 2000, In Saccharomyces cerevisiae, expression of arginine catabolic genes CAR1 and CAR2 in response to exogenous nitrogen availability is mediated by the Ume6 (CargRI)-Sin3 (CargRII)-Rpd3 (CargRIII) complex, J. Bacteriol., 182, 3158-3164.