Livas et al. BMC Genomics 2011, 12:405 http://www.biomedcentral.com/1471-2164/12/405 gene features. The Significance Analysis of Microarrays (SAM version 3.0) add-in to Microsoft Excel was used for comparisons of duplicate array experiments [55] SAM assesses the difference between two mean values when taking into account the standard errors of those means. The significance of that difference is estimated by comparing it against the probability of its occurrence by chance alone. The model of chance occurrence is generated by permutation of the input data, rather than a predetermined model (e.g. a normal distribution), as is used by the t-test. The transcript data can be downloaded from Genome Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under the series accession number GSE27541. RT-qPCR measurements The RNA samples were treated with DNase I (Ambion) and the quality of the purified RNA checked using the Agilent 2100 Bioanalyzer. The oligonucleotides used for RT-qPCR are shown in table 7. The measurements were performed in triplicate using SYBR green I. Normaliza- tion was carried out with the 18S rRNA. List of abbreviations PCR: polymerase chain reaction; PKA: protein kinase A; RT-qPCR: quantitative real-time polymerase chain reaction; YNB: Yeast Nitrogen Base. Acknowledgements We thank Carlos Gancedo for a thorough revision of the manuscript and Cecile Brocard (University of Vienna) for kindly providing yeast strains. This work was supported by Grant BFU2007-66063-C02-01/BMC from the Spanish Ministry of Science and Innovation (MICINN). DL was a pre-doctoral fellow from the Conacyt (Mexico). The Kluyver Centre for Genomics of Industrial Fermentation is sponsored by the Netherlands Genomics Initiative. Author details 1Department of Metabolism and Cell Signalling, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Arturo Duperier 4, 28029 Madrid, Spain. 2Department of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics and Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands. Authors’ contributions DL performed the cultures, collected the yeast samples and extracted RNA. MA performed the microarray experiments. JMD analysed the microarray data. JTP co-designed the experiments and contributed to the writing. JMG conceived the study, designed experiments, constructed yeast strains, analysed data and wrote the paper. All authors discussed the results and read and approved the final manuscript. Received: 15 April 2011 Accepted: 9 August 2011 Published: 9 August 2011 References 1. van der Plaat JB: Cyclic 3’,5’-adenosine monophosphate stimulates trehalose degradation in baker’s yeast. Biochem Biophys Res Commun 1974, 56:580-587. 2. 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