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PROPHECY--a yeast phenome database, update 2006.

Fernandez-Ricaud L, Warringer J, Ericson E, Glaab K, Davidsson P, Nilsson F, Kemp GJ, Nerman O, Blomberg A - Nucleic Acids Res. (2006)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University, Medicinaregatan 9c SE-41390 Göteborg, Sweden.

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.

Show MeSH
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.
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fig3: 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.

Mentions: PROPHECY integrates phenotype data with other features, notably protein localization and functional annotation, by using a Filter tool. The Filter capabilities that are part of the Advanced Query facility have been extended in several ways (Figure 3). After selecting all 4711 mutants and all environments, one can filter for specific features that are of particular interest, e.g. one can select mutants that show a statistically significant rate phenotype in any of the environments (brings down the number to 2084), where the encoded protein is localized to the cytoplasm (brings down the number to 953) and is involved in ribosome biogenesis (final number of gene-deletions is 100). Thus, one can filter for classes of proteins that are of particular interest and integrate phenotypes with other types of relevant information.


PROPHECY--a yeast phenome database, update 2006.

Fernandez-Ricaud L, Warringer J, Ericson E, Glaab K, Davidsson P, Nilsson F, Kemp GJ, Nerman O, Blomberg A - Nucleic Acids Res. (2006)

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.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1761427&req=5

fig3: 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.
Mentions: PROPHECY integrates phenotype data with other features, notably protein localization and functional annotation, by using a Filter tool. The Filter capabilities that are part of the Advanced Query facility have been extended in several ways (Figure 3). After selecting all 4711 mutants and all environments, one can filter for specific features that are of particular interest, e.g. one can select mutants that show a statistically significant rate phenotype in any of the environments (brings down the number to 2084), where the encoded protein is localized to the cytoplasm (brings down the number to 953) and is involved in ribosome biogenesis (final number of gene-deletions is 100). Thus, one can filter for classes of proteins that are of particular interest and integrate phenotypes with other types of relevant information.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University, Medicinaregatan 9c SE-41390 Göteborg, Sweden.

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.

Show MeSH