Genome-wide expression analysis is being used to obtain clues to the roles played by transcriptional regulators, components of the transcription initiation apparatus, histones and chromatin-modifying enzymes in gene regulation. Previous genetic and biochemical studies identified much of the transcriptional machinery of eukaryotic cells and provided mechanistic insights into the functions of various components at specific promoters. However, knowledge of the contributions of regulators and the transcriptional machinery to the complete transcriptional circuitry is lacking. Our data describes how expression of the genome depends on over 50 components critical to transcriptional regulation in yeast cells. This information provides a foundation for understanding the molecular mechanisms involved in genome-wide expression, and new insights into transcriptional regulation will be described.