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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.

Ståhlberg A, Elbing K, Andrade-Garda JM, Sjögreen B, Forootan A, Kubista M - BMC Genomics (2008)

Bottom Line: In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc.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.The technique also identifies genes that show perturbed expression in specific strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: TATAA Biocenter, Odinsgatan 28, 411 03 Göteborg, Sweden. anders.stahlberg@neuro.gu.se

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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Related in: MedlinePlus

Classification of genes using PCA. The FC (A) and FCAS(B) over time are shown for wild-type yeast. Using PCA the first three scores vectors (C) are shown together with PC1-PC2 (D) and PC1-PC2-PC3 (E) plots for wild-type yeast. Corresponding PC1-PC2 plots are shown for the HXT-HXT7 (F), HXT-TM6* (G), and HXT- (H) strains. The following colors and symbols are used: Glucose-induced genes (blue), glucose-repressed genes (red), ADH3-6 (yellow), HSP12 (black), CYC1 (green), wild-type (circles), HXT-HXT7 (squares), HXT-TM6* (triangles) and HXT- (stars).
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Figure 4: Classification of genes using PCA. The FC (A) and FCAS(B) over time are shown for wild-type yeast. Using PCA the first three scores vectors (C) are shown together with PC1-PC2 (D) and PC1-PC2-PC3 (E) plots for wild-type yeast. Corresponding PC1-PC2 plots are shown for the HXT-HXT7 (F), HXT-TM6* (G), and HXT- (H) strains. The following colors and symbols are used: Glucose-induced genes (blue), glucose-repressed genes (red), ADH3-6 (yellow), HSP12 (black), CYC1 (green), wild-type (circles), HXT-HXT7 (squares), HXT-TM6* (triangles) and HXT- (stars).

Mentions: The temporal expression profiles, expressed as FC, are shown for the wild-type strain in Figure 4A. To give all genes equal weights for classification of expression profiles the data were autoscaled (FCAS) by subtracting the mean expression of every gene in each strain (i.e, the column mean) and dividing with the (column) standard deviation:


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

Ståhlberg A, Elbing K, Andrade-Garda JM, Sjögreen B, Forootan A, Kubista M - BMC Genomics (2008)

Classification of genes using PCA. The FC (A) and FCAS(B) over time are shown for wild-type yeast. Using PCA the first three scores vectors (C) are shown together with PC1-PC2 (D) and PC1-PC2-PC3 (E) plots for wild-type yeast. Corresponding PC1-PC2 plots are shown for the HXT-HXT7 (F), HXT-TM6* (G), and HXT- (H) strains. The following colors and symbols are used: Glucose-induced genes (blue), glucose-repressed genes (red), ADH3-6 (yellow), HSP12 (black), CYC1 (green), wild-type (circles), HXT-HXT7 (squares), HXT-TM6* (triangles) and HXT- (stars).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2335116&req=5

Figure 4: Classification of genes using PCA. The FC (A) and FCAS(B) over time are shown for wild-type yeast. Using PCA the first three scores vectors (C) are shown together with PC1-PC2 (D) and PC1-PC2-PC3 (E) plots for wild-type yeast. Corresponding PC1-PC2 plots are shown for the HXT-HXT7 (F), HXT-TM6* (G), and HXT- (H) strains. The following colors and symbols are used: Glucose-induced genes (blue), glucose-repressed genes (red), ADH3-6 (yellow), HSP12 (black), CYC1 (green), wild-type (circles), HXT-HXT7 (squares), HXT-TM6* (triangles) and HXT- (stars).
Mentions: The temporal expression profiles, expressed as FC, are shown for the wild-type strain in Figure 4A. To give all genes equal weights for classification of expression profiles the data were autoscaled (FCAS) by subtracting the mean expression of every gene in each strain (i.e, the column mean) and dividing with the (column) standard deviation:

Bottom Line: In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc.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.The technique also identifies genes that show perturbed expression in specific strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: TATAA Biocenter, Odinsgatan 28, 411 03 Göteborg, Sweden. anders.stahlberg@neuro.gu.se

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.

Show MeSH
Related in: MedlinePlus