PROPHECY--a database for high-resolution phenomics

Abstract

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.

Figure 1

The Advanced Query data selection process: overview of the Advanced Query process in PROPHECY that is designed to guide the user through the selection criteria in a wizard/assistant based fashion via a linear querying process by (i) selecting a dataset, (ii) selecting strains/genes and (iii) selecting environmental stress conditions. Phenotypic data can then be displayed at different levels of abstraction (LPI, LSC and growth variables and curves). The resulting sets can be filtered by degree of growth defect or functional classification.

Figure 2

The different levels of data display: data output formats following the Advanced Query. Data are presented at progressively lower levels of abstraction: (a) the graphical Compact LPI Display, (b) the Tabular LPI Display, (c) the Tabular LSC Display, (d) the Individual Growth Variables and Curves display and (e) the Growth Curve Comparison Tool display (activated by clicking on the growth curve thumbnails).

Figure 3

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. Deletion strains are represented by red growth curves, representative reference strain by black curves. Gene names in red indicate significant (LSC < 0; P < 0.001) phenotypes. Yellow circles indicate strains not present in the yeast deletion strain collection.

Figure 4

Integrating gene dispensability and protein complex data: visualizing robustness within protein complexes by integrating MIPS protein complex data with PROPHECY gene dispensability data. The protein complex catalogue can be filtered by the degree of phenotypic homogeneity in the complex. The robustness of the protein complexes are classified according to the majority of phenotypes scored for the removal of individual complex components.