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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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Hierarchical clustering of the genes in the wild-type, HXT-HXT7 and HXT-TM6* strains. Un-weighted pairs were used to calculate similarities between clusters based on Euclidian distances. Five different groups are identified and marked in the plot.
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Figure 6: Hierarchical clustering of the genes in the wild-type, HXT-HXT7 and HXT-TM6* strains. Un-weighted pairs were used to calculate similarities between clusters based on Euclidian distances. Five different groups are identified and marked in the plot.

Mentions: Figure 6 shows the graphical output (dendrogram) of the hierarchical clustering of the catenated wild-type, HXT-HXT7 and HXT-TM6* autoscaled data, using the Euclidean distance to measure similarity and the unweighted pairs clustering algorithm [40]. The dendrogram reveals four main groups: from top, the first group is composed of MDH2, FBP1, HSP12 and ADH2 from all three strains, SUC2 from HXT-HXT7, ADH3 from wild-type and HXT-HXT7, and ADH5 from wild-type. Group 2 contains CYC1 from all strains together with SUC2 from wild-type and ADH5 from HXT-TM6* and HXT-HXT7 and ADH3 from HXT-TM6*. Group 3 contains all ADH6 and ADH4 from wild-type and HXT-HXT7, and PGK1 and MIG1 from HXT-HXT7. Last group contains all TPI1, ADH1, and PDC1, together with MIG1 from wild-type and HXT-TM6*, PGK1 from the wild-type and ADH4 from HXT-TM6*. PGK1 in HXT-TM6* belongs to no group evidencing it has a unique response. The four groups as well as the unique location of PGK1 in HXT-TM6* agree well with the four regions in the PC1 vs. PC2 loadings scatter plot of the PCA shown above (Figure 5) reinforcing the previous conclusions.


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)

Hierarchical clustering of the genes in the wild-type, HXT-HXT7 and HXT-TM6* strains. Un-weighted pairs were used to calculate similarities between clusters based on Euclidian distances. Five different groups are identified and marked in the plot.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Hierarchical clustering of the genes in the wild-type, HXT-HXT7 and HXT-TM6* strains. Un-weighted pairs were used to calculate similarities between clusters based on Euclidian distances. Five different groups are identified and marked in the plot.
Mentions: Figure 6 shows the graphical output (dendrogram) of the hierarchical clustering of the catenated wild-type, HXT-HXT7 and HXT-TM6* autoscaled data, using the Euclidean distance to measure similarity and the unweighted pairs clustering algorithm [40]. The dendrogram reveals four main groups: from top, the first group is composed of MDH2, FBP1, HSP12 and ADH2 from all three strains, SUC2 from HXT-HXT7, ADH3 from wild-type and HXT-HXT7, and ADH5 from wild-type. Group 2 contains CYC1 from all strains together with SUC2 from wild-type and ADH5 from HXT-TM6* and HXT-HXT7 and ADH3 from HXT-TM6*. Group 3 contains all ADH6 and ADH4 from wild-type and HXT-HXT7, and PGK1 and MIG1 from HXT-HXT7. Last group contains all TPI1, ADH1, and PDC1, together with MIG1 from wild-type and HXT-TM6*, PGK1 from the wild-type and ADH4 from HXT-TM6*. PGK1 in HXT-TM6* belongs to no group evidencing it has a unique response. The four groups as well as the unique location of PGK1 in HXT-TM6* agree well with the four regions in the PC1 vs. PC2 loadings scatter plot of the PCA shown above (Figure 5) reinforcing the previous conclusions.

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