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PROPHECY


NAR Molecular Biology Database Collection entry number 730
Fernandez-Ricaud L.1, Warringer J.1, Ericson E.1, Glaab K.1, Davidsson P.1, Nilsson F1, Kemp G.J.L.3, Nerman O.2 and Blomberg A.1
1 Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University Medicinaregatan 9c, 41390 Göteborg, Sweden
2 Department of Mathematical Statistics, Chalmers University of Technology, SE-41296 Göteborg, Sweden
3 Department of Computer Science and Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden

Database Description

Connecting genotype to phenotype is of fundamental importance in biomedical research and in our understanding of disease. Phenomics - large-scale analysis of gene function by quantitative analysis of phenotypes on a genome-wide scale - connects automated phenotype data generation of mutants with the development of novel tools for phenotype data integration, mining and visualization. Following the introduction of a novel approach for precise, high-resolution, genome-wide quantification of gene dispensability in Saccharomyces cerevisiae PROPHECY is an initiative and a database aimed at enhancing the growing field of phenome bioinformatics. PROPHECY is designed to allow easy and flexible access to physiologically relevant quantitative data for the growth behaviour of mutant strains, mainly in the yeast deletion collection BY4742. Mutants are also analysed during conditions of environmental challenges with the aim to provide data on gene-by-environment interaction for all yeast genes to a large number of conditions, currently including basal medium with addition of NaCl, paraquat, diamide or DTT.

Recent Developments

The number of genes for which phenotypic information are provided has been extended to include all yeast genes by the phenotyping of 984 heterozygous diploids for the essential genes. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate 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 to 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.

Acknowledgements

The creation a maintenance of PROPHECY has been financially supported by the Swedish Research Council (VR) and the Swedish Foundation of Strategic Research (SSF). Luciano Fernadez-Ricaud is supported by the National Research School in Genomics and Bioinformatics.

References

1. Warringer, J., and Blomberg, A. (2003) Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. YEAST, 20: 53-67
2. Warringer, J., Ericson, E., Fernandez-Ricaud, L., Nerman, O., and Blomberg, A. (2003) High-resolution yeast phenomics resolves different physiological features of the saline response. Proc. Natl. Acad.f Sci. USA, 100: 15724-15729.
3. Fernandez-Ricaud, L., Warringer, J., Ericson, E., Pylvänäinen, I., Kemp, G., Nerman, O., and Blomberg, A. (2005) PROPHECY - a database for high-resolution phenomics. Nucleic Acid Res. 33: D369-D373.
4. Österberg, M, Kim, H., Warringer, J, Melén, K., Blomberg, A., Von Heijne, G. (2006) Phenotypic effects of membrane protein overexpression in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA, 103:11148-11153.


Go to the abstract in the NAR 2007 Database Issue.
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