Promoter analysis of co-regulated genes in the yeast genome

The use of high density DNA arrays to monitor gene expression at a genome-w ide scale constitutes a fundamental advance in biology. In particular, the expression pattern of all genes in Saccharomyces cerevisiae can be interrog ated using microarray analysis where cDNAs are hybridized to an array of mo re than 6000 genes in the yeast genome. In an effort to build a comprehensi ve Yeast Promoter Database and to develop new computational methods for map ping upstream regulatory elements, we started recently in an on going colla boration with experimental biologists on analysis of large-scale expression data. It is well known that complex gene expression patterns result from d ynamic interacting networks of genes in the genetic regulatory circuitry. H ierarchical and modular organization of regulatory DNA sequence elements ar e important information for our understanding of combinatorial control of g ene expression. As a bioinformatics attempt in this new direction, we have done some computational exploration of various initial experimental data. W e will use cell-cycle regulated gene expression as a specific example to de monstrate how one may extract promoter information computationally from suc h genome-wide screening. Full report of the experiments and of the complete analysis will be published elsewhere when all the experiments are to be fi nished later in this year (Spellman, P.T., et al. 1998. Mol. Biol. Cell 9, 3273-3297). (C) 1999 Elsevier Science Ltd. All rights reserved.