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Series GSE33097 Query DataSets for GSE33097
Status Public on Jun 18, 2012
Title Deletion mutant analysis of established glucose signaling and metabolic pathway members in Saccharomyces cerevisiae
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary To understand the organisation of the glucose regulatory system, we analysed 91 deletion mutants of established glucose signalling and metabolic pathway members in Saccharomyces cerevisiae by DNA microarrays. These deletion mutants do not induce pathway-specific transcriptional responses reflecting the tight interconnection between pathways of the glucose regulatory system. Instead, one main transcriptional response is discerned, which varies in direction to mimic either a high or a low glucose response. The study reveals both known and unknown relationships within and between individual pathways and their members. Metabolic components of the glucose regulatory system are most frequently affected at the transcriptional level. A new network approach is applied that exposes the hierarchical organisation of the glucose regulatory system. Tps2 and Tsl1, two enzymes involved in trehalose biosynthesis, are predicted to be the most downstream transcriptional components. This prediction is further validated by epistasis analysis of Tps2 double mutants. Taken together, this suggests that changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.
 
Overall design RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used for each separate hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Up to five deletion strains were grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.
 
Contributor(s) Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker L, van Leenen D, Holstege F, Kemmeren P
Citation(s) 22697265
Submission date Oct 19, 2011
Last update date Nov 07, 2015
Contact name Patrick Kemmeren
Organization name UMC Utrecht
Department Department of Molecular Cancer Research
Lab Holstege Lab
Street address Universiteitsweg 100
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CG
Country Netherlands
 
Platforms (1)
GPL11232 A-UMCU-Y16k-1.3
Samples (295)
GSM630135 elm1-del-3-a
GSM630136 elm1-del-3-b
GSM630223 pkh1-del-1-a
This SubSeries is part of SuperSeries:
GSE33099 Glucose signaling
Relations
BioProject PRJNA156577

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
GSE33097_Final_Gene_Expression_Matrix.txt.gz 11.1 Mb (ftp)(http) TXT
GSE33097_RAW.tar 195.5 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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