PROPHECY—a database for high-resolution phenomics

The rapid recent evolution of the field phenomics—the genome-wide study of gene dispensability by quantitative analysis of phenotypes—has resulted in an increasing demand for new data analysis and visualization tools. Following the introduction of a novel approach for precise, genome-wide quantification of gene dispensability in Saccharomyces cerevisiae we here announce a public resource for mining, filtering and visualizing phenotypic data—the PROPHECY database. PROPHECY is designed to allow easy and flexible access to physiologically relevant quantitative data for the growth behaviour of mutant strains in the yeast deletion collection during conditions of environmental challenges. PROPHECY is publicly accessible at http://prophecy.lundberg.gu.se

Genetic pleiotropy in Saccharomyces cerevisiae quantified by high-resolution phenotypic profiling

Genetic pleiotropy, the ability of a mutation in a single gene to give rise to multiple phenotypic outcomes, constitutes an important but incompletely understood biological phenomenon. We used a highresolution and high-precision phenotypic profiling approach to quantify the fitness contribution of genes on the five smallest yeast chromosomes during different forms of environmental stress, selected to probe a wide diversity of physiological features. We found that the extent of pleiotropy is much higher than previously claimed; 17% of the yeast genes were pleiotropic whereof one-fifth were hyper-pleiotropic. Pleiotropic genes preferentially participate in functions related to determination of protein fate, cell growth and morphogenesis, signal transduction and transcription. Contrary to what has earlier been proposed we did not find experimental evidence for slower evolutionary rate of pleiotropic genes/proteins. We also refute the existence of phenotypic islands along chromosomes but report on a remarkable loss both of pleiotropy and of phenotypic penetrance towards chromosomal ends. Thus, the here reported features of pleiotropy both have implications on our understanding of evolutionary processes as well as the mechanisms underlying disease

Functional classification filtering allows dissection of biochemical pathways: visualizing the growth behaviour of the components of a signalling pathway—the HOG pathway—during saline stress

<p><b>Copyright information:</b></p><p>Taken from "PROPHECY—a database for high-resolution phenomics"</p><p>Nucleic Acids Research 2004 ;33(Database Issue):D369-D373.</p><p>Published online 17 Dec 2004 </p><p>PMCID:PMC540080.</p><p>Copyright © 2005 Oxford University Press</p> Deletion strains are represented by red growth curves, representative reference strain by black curves. Gene names in red indicate significant (LSC < 0; < 0.001) phenotypes. Yellow circles indicate strains not present in the yeast deletion strain collection