PROPHECY--a yeast phenome database, update 2006

Abstract

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics--the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale--connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization. Our yeast phenomics database PROPHECY is available at http://prophecy.lundberg.gu.se. Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate the interpretation of quantitative phenotypic data we have developed a new phenotype display option, the Comparative Growth Curve Display, where growth curve differences for a large number of mutants compared with the wild type are easily revealed. In addition, PROPHECY now offers a more informative and intuitive first-sight display of its phenotypic data via its new summary page. We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics.

Figure 1

Compact Comparative Growth Curve Display. As a part of the Advanced Query facility multiple mutants under many environmental conditions can be visualized in a compact way. In this particular case some of the heterozygous diploids of essential genes exhibiting statistically significant phenotype have been selected and their compact comparative growth curve displays are presented.

Figure 2

Example for Phenotypic summary page. This page is the output from a quick search from the PROPHECY home page or via linking from the SGD Locus Page. From the summary page the user is directed to the Advanced Query tool.

Figure 3

Data filtering and integration. The filtering tool provides several means of integrating phenotypic information with features such as protein localization and annotation. (A) Clicking on the Filter button opens a page where specific features can be selected. Note that the Filter tool is context dependent and will therefore contain different filtering options depending on the level of abstraction being used as the start point. (B) An example of a filtering procedure for mutants with a significant rate phenotype in any of several stress environments and where the encoded protein is annotated as involved in ribosome biogenesis.

Figure 4

Clumping of phenotypes along chromosomes. In this display certain regions on specific chromosomes can be selected and enlarge for better visualization of phenotypic similarities between neighbouring gene.