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Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli.

Journal article
Authors Anders Ståhlberg
Karin Elbing
José Manuel Andrade-Garda
Björn Sjögreen
Amin Forootan
Mikael Kubista
Published in BMC genomics
Volume 9
Pages 170
ISSN 1471-2164
Publication year 2008
Published at Department of Cell and Molecular Biology
Institute of Neuroscience and Physiology, Department of Clinical Neuroscience and Rehabilitation
Pages 170
Language en
Links dx.doi.org/10.1186/1471-2164-9-170
Keywords Alcohol Dehydrogenase, metabolism, Gene Expression Profiling, methods, Glucose, pharmacology, Models, Biological, Principal Component Analysis, Reverse Transcriptase Polymerase Chain Reaction, Saccharomyces cerevisiae, genetics, metabolism, Species Specificity, Transcription, Genetic, drug effects
Subject categories Mathematical statistics, Biological Sciences

Abstract

BACKGROUND: The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions. RESULTS: We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition. CONCLUSION: Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains.

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