Open Access Research article

Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains

Laura Carreto12, Maria F Eiriz1, Inês Domingues1, Dorit Schuller3, Gabriela R Moura1 and Manuel AS Santos1*

Author Affiliations

1 RNA Biology Laboratory, CESAM & Department of Biology, Universidade de Aveiro, 3810-193 Aveiro, Portugal

2 BIOCANT, Centro de Inovação em Biotecnologia, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 3, 3060-197 Cantanhede, Portugal

3 Centro de Biologia Molecular e Ambiental (CBMA) Universidade do Minho, Braga, Portugal

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BMC Genomics 2011, 12:201  doi:10.1186/1471-2164-12-201

Published: 20 April 2011

Additional files

Additional file 1:

Cell viability. Cell viability during fermentation was compared for Saccharomyces cerevisiae strains Lalvin EC-1118, 06L3FF02, J940047 and S288C.

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Additional file 2:

Co-expression cluster line graphs. Gene co-expression was investigated for strains 06L3FF02, 06L6FF20, AEB Fermol Rouge, Lalvin ICV D254, Lalvin EC-1118, J940047 and S288C from the measurements of relative transcript abundance during fermentation. Graphs represent the average relative transcript abundance (log2 ratio) determined for groups of genes having highly correlated expression profiles across samples.

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Additional file 3:

Relevant aCGH data. Summary of gene copy number differences observed between the Saccharomyces cerevisiae strains included in this study. Relative gene copy number values (fold change relatively to strain S288C) were obtained by comparative genome hybridization on array (Carreto et al. 2008. BMC Genomics 9: 524). Only genes relevant for discussion in the present manuscript were represented.

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Additional file 4:

Variability in TATA box genes. Variability in gene expression was biased towards TATA box genes. The graphics show the frequency of TATA box genes as a function of gene expression variability. The average deviation from the mean of the relative gene expression value was taken as a measure of expression variability. Panel A was obtained considering all the investigated strains while Panel B represents the distribution obtained for the environmental and commercial strains.

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Additional file 5:

GO Biological Process enrichment in top variable genes. Results obtained from a Gene ontology (GO) term enrichment analysis performed to determine the over-representation of Biological Processes among the top variable genes (FatiScan). The list of genes was ranked according to the average deviation from the mean relative expression measured among the yeast strains studied.

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Additional file 6:

Correlation between gene expression and aCGH. Correlation between relative transcript abundance and putative differences in gene load was found for some genes. The relative transcript abundance values determined for each strain relatively to those of strain S288C were plotted against the relative gene copy number differences for the same strains. The analysis was performed using the datasets from T2 (Panel A) and T4 (Panel B) stages of fermentation.

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