Using an integrated genomic and proteomic approach, we have investigated the effects of carbon source perturbation on steady-state gene expression in the yeast Saccharomyces cerevisiae growing on either galactose or ethanol. For many genes, significant differences between the abundance ratio of the messenger RNA transcript and the corresponding protein product were observed. Insights into the perturbative effects on genes involved in respiration, energy generation, and protein synthesis were obtained that would not have been apparent from measurements made at either the messenger RNA or protein level alone, illustrating the power of integrating different types of data obtained from the same sample for the comprehensive characterization of biological systems and processes. Molecular & Cellular Proteomics 1:323-333,
2002.The concept of discovery science, best illustrated by the human genome project (1, 2), involves the identification of the components of a system without the prior formulation of hypotheses as to how these components function (3). This scientific method has spawned what has become known as the "systems" approach to biology, which involves the comprehensive characterization of the components of a biological system (i.e. DNA, RNA, and proteins) as a whole, leading to insights into the responses of these components because of systematic perturbations to the system. The objective of the systems biology approach is to identify markers and mechanisms that are important to the function of the perturbed system, with the ultimate goal of developing computational models that enable the prediction of the response of the system to any given perturbation.Traditionally, studies measuring the effects of systematic perturbations have been carried out at the level of transcribed mRNA, most commonly using cDNA arrays and chip technologies (4 -7), or alternative methods for mRNA analysis such as serial analysis of gene expression (8), differential display (9), and cDNA fingerprinting (10). These technologies have been used to distinguish diagnostically between cell types (7,(11)(12)(13)(14)(15) and to differentiate between states (metabolic, activation, pathological) of a particular cell type (6, 16), as well as for the comprehensive analysis of cellular pathways and processes by targeted perturbations of cells (16 -19).Although the measurement of transcribed mRNA has proven to be very powerful in the discovery of molecular markers and the elucidation of functional mechanisms, alone it is not sufficient for the characterization of biological systems as a whole. This is based on several observations. First, comparison of absolute mRNA transcript abundances measured by serial analysis of gene expression (8) with the corresponding protein abundances expressed in exponentially growing Saccharomyces cerevisiae cells has shown that in many cases mRNA abundance is not a reliable indicator of corresponding protein abundance (20), and studies in other systems have reached similar conclusions (21, 22). Furthermore, attenuation...