We use algorithmic and visualisation approaches to study the gene expression data for the complete yeast genome in the transition from fermentation to respiration. We treat the expression measurements as time series and study to what extent the gene expression profiles correlate with the gene functional annotations as given in MIPS database. We also hypothesize that genes with similar expression profiles are likely to be regulated by similar regulation mechanisms, and that consequently their promoters may share similarities. We use sequence pattern discovery algorithms to study such promoters and find that they contain common elements similar to known transcription factor binding sites.