journal article Apr 08, 2007

Genetic reconstruction of a functional transcriptional regulatory network

Topics

No keywords indexed for this article. Browse by subject →

References
29
[1]
Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002). 10.1126/science.1075090
[2]
Transcriptional regulatory code of a eukaryotic genome

Christopher T. Harbison, D. Benjamin Gordon, Tong Ihn Lee et al.

Nature 2004 10.1038/nature02800
[3]
Sekinger, E.A. & Gross, D.S. Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105, 403–414 (2001). 10.1016/s0092-8674(01)00329-4
[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). 10.1016/j.molcel.2005.03.010
[5]
Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109–126 (2000). 10.1016/s0092-8674(00)00015-5
[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). 10.1038/ng569
[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). 10.1128/mcb.24.12.5249-5256.2004
[8]
Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001). 10.1038/35054095
[9]
Van Driessche, N. et al. Epistasis analysis with global transcriptional phenotypes. Nat. Genet. 37, 471–477 (2005). 10.1038/ng1545
[10]
Yeang, C.H. et al. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 6, R62 (2005). 10.1186/gb-2005-6-7-r62
[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). 10.1142/9789814447362_0042
[12]
Mnaimneh, S. et al. Exploration of essential gene functions via titratable promoter alleles. Cell 118, 31–44 (2004). 10.1016/j.cell.2004.06.013
[13]
Zhu, J. & Zhang, M.Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15, 607–611 (1999). 10.1093/bioinformatics/15.7.607
[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). 10.1186/gb-2003-4-7-r43
[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). 10.1038/nature01644
[16]
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

Frederick P. Roth, Jason D. Hughes, Preston W. Estep et al.

Nature Biotechnology 1998 10.1038/nbt1098-939
[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).
[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). 10.1038/nbt717
[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). 10.1074/jbc.m409012200
[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). 10.1083/jcb.151.4.863
[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). 10.1038/ng1165
[22]
Simon, I. et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697–708 (2001). 10.1016/s0092-8674(01)00494-9
[23]
Rosenfeld, N. & Alon, U. Response delays and the structure of transcription networks. J. Mol. Biol. 329, 645–654 (2003). 10.1016/s0022-2836(03)00506-0
[24]
Hall, D.A. et al. Regulation of gene expression by a metabolic enzyme. Science 306, 482–484 (2004). 10.1126/science.1096773
[25]
Sopko, R. et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21, 319–330 (2006). 10.1016/j.molcel.2005.12.011
[26]
Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999). 10.1126/science.285.5429.901
[27]
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale

Joseph L. DeRisi, Vishwanath R. Iyer, Patrick O. Brown

Science 1997 10.1126/science.278.5338.680
[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). 10.1186/1471-2105-4-32
[29]
Eisen, M.B. & Brown, P.O. DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179–205 (1999). 10.1016/s0076-6879(99)03014-1
Cited By
377
Addressing false discoveries in network inference

Tobias Petri, Stefan Altmann · 2015

Bioinformatics
Physical Review E
PLOS Genetics
Birth Defects Research Part C: Embr...
Metrics
377
Citations
29
References
Details
Published
Apr 08, 2007
Vol/Issue
39(5)
Pages
683-687
License
View
Cite This Article
Zhanzhi Hu, Patrick J Killion, Vishwanath R Iyer (2007). Genetic reconstruction of a functional transcriptional regulatory network. Nature Genetics, 39(5), 683-687. https://doi.org/10.1038/ng2012
Related

You May Also Like

Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball · 2000

43,924 citations

The Genotype-Tissue Expression (GTEx) project

John Lonsdale, Jeffrey Thomas · 2013

8,263 citations

The Cancer Genome Atlas Pan-Cancer analysis project

John N Weinstein, Eric A Collisson · 2013

7,845 citations