Reference: Hoehndorf R, et al. (2013) Systematic analysis of experimental phenotype data reveals gene functions. PLoS One 8(4):e60847

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Abstract


High-throughput phenotyping projects in model organisms have the potential to improve our understanding of gene functions and their role in living organisms. We have developed a computational, knowledge-based approach to automatically infer gene functions from phenotypic manifestations and applied this approach to yeast (Saccharomyces cerevisiae), nematode worm (Caenorhabditis elegans), zebrafish (Danio rerio), fruitfly (Drosophila melanogaster) and mouse (Mus musculus) phenotypes. Our approach is based on the assumption that, if a mutation in a gene [Formula: see text] leads to a phenotypic abnormality in a process [Formula: see text], then [Formula: see text] must have been involved in [Formula: see text], either directly or indirectly. We systematically analyze recorded phenotypes in animal models using the formal definitions created for phenotype ontologies. We evaluate the validity of the inferred functions manually and by demonstrating a significant improvement in predicting genetic interactions and protein-protein interactions based on functional similarity. Our knowledge-based approach is generally applicable to phenotypes recorded in model organism databases, including phenotypes from large-scale, high throughput community projects whose primary mode of dissemination is direct publication on-line rather than in the literature.

Reference Type
Journal Article | Research Support, N.I.H., Extramural | Research Support, Non-U.S. Gov't
Authors
Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV
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Gene Ontology Annotations


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Gene/Complex Qualifier Gene Ontology Term Aspect Annotation Extension Evidence Method Source Assigned On Reference

Phenotype Annotations


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Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

Disease Annotations


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Gene Disease Ontology Term Qualifier Evidence Method Source Assigned On Reference

Regulation Annotations


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Regulator Target Direction Regulation Of Happens During Method Evidence

Post-translational Modifications


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Site Modification Modifier Reference

Interaction Annotations


Genetic Interactions

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Interactor Interactor Allele Assay Annotation Action Phenotype SGA score P-value Source Reference

Physical Interactions

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Interactor Interactor Assay Annotation Action Modification Source Reference

Functional Complementation Annotations


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Gene Species Gene ID Strain background Direction Details Source Reference