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Series GSE10146 Query DataSets for GSE10146
Status Public on Feb 04, 2008
Title A systems approach to delineate functions of YAP family members
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Genome binding/occupancy profiling by genome tiling array
Summary Duplication of genes encoding transcription factors plays an essential role in driving phenotypic variation.
Because regulation can occur at multiple levels, it is often difficult to discern how each duplicated factor achieves its regulatory specificity.
In these cases, a systems approach may distinguish the role of each factor by integrating complementary large-scale measurements of the regulatory network.
To explore such an approach, we integrate growth phenotypes, promoter binding profiles, and gene expression patterns to model the DNA damage response network controlled by the Yeast-specific AP-1 (YAP) family of transcription factors.
This analysis reveals that YAP regulatory specificity is achieved by at least three mechanisms: (a) Divergence of DNA-binding sequences into two subfamilies; (b) Condition-specific combinatorial regulation by multiple Yap factors; and (c) Interactions of Yap 1, 4, and 6 with chromatin remodeling proteins.
Additional microarray experiments establish that Yap4 and 6 regulate gene expression through interactions with the histone deacetylase, Hda1.
The data further highlight differences among Yap paralogs in terms of their regulatory mode of action (activation vs. repression).
This study suggests how other large TF families might be disentangled in the future.
Keywords: gene expression microarray and ChIP-chip
 
Overall design Gene expression of wild type and single YAP deletion (YAP1/2/4/5/6) strains were profiled in media supplemented with either MMS or CDDP at two different concentrations. ChIP-chip of five YAPs (YAP1/2/4/6/6) were done in duplicate in both drug-treated (MMS or CDDP) or untreated (SC media) conditions.
 
Contributor(s) Tan K, Feizi H, Luo C, Fan S, Ravasi T, Ideker T
Citation(s) 18287073
Submission date Jan 11, 2008
Last update date Dec 06, 2012
Contact name Kai Tan
Organization name University of California San Diego
Department Bioengineering
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (2)
GPL884 Agilent-011447 Yeast Oligo Microarray G4140A (Feature Number version)
GPL3737 Agilent-012713 Yeast Whole Genome ChIP-on-chip Microarray (G4486A)
Samples (110)
GSM255865 YAP4-TAP 1.4mM CDDP treatment replicate 1
GSM255866 YAP4-TAP 1.4mM CDDP treatment replicate 2
GSM255867 YAP4-TAP 0.4mM CDDP treatment replicate 1
Relations
BioProject PRJNA108695

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10146_RAW.tar 363.1 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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