Microarrays and gene regulation networks in yeast

The development of DNA microarrays has provided considerable impetus to research on genetic regulatory networks since it has enabled genome¬wide snapshots of the cellular response to physiological changes. This has led to a revolution in the speed and scope of genetic analysis of regulatory networks, nowhere more so than in the yeast Saccharomyces cerevisiae due to the relatively small size of this organism's genome, the speed with which genetic analysis can be undertaken and the availability of a wide range of genomic tools. These tools include the collection of deletion mutants covering all of the nonessential genes in yeast, the extensive databases of protein¬protein interactions, clones for expression in yeast of almost all of its genes as well as the accumulated data from many hundreds of microarray studies. These microarray studies have encompassed gene expression during cellular processes such as cell division, meiosis and spore formation as well as cellular responses to altered nutrient conditions, a wide range of stresses and drug treatments. In some of these analyses mutants with specific defects in signal transduction pathways, or in specific transcription factors have been exploited to provide information about the control systems operating to effect the changes in transcription patterns. The purpose of this chapter is to review the main techniques that are available in yeast studies to identify cellular control networks and how they interact with each other as one component of the field now called Systems Biology. Yeast has been preeminent in these developments and these studies have provided the paradigm for extending network analysis to other, more complex organisms, especially mouse and human.