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Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution
Prashanti Manda1,2, James P Balhoff1,2, Hilmar Lapp2,3
1Department of Biology, University of North Carolina, Chapel Hill, North Carolina.
Genesis (New York, N.Y. : 2000)
|July 30, 2015
Summary
The Phenoscape Knowledgebase (KB) links genetic variation in model organisms to natural phenotypic diversity across species. This tool aids in understanding evolutionary phenotypes by comparing gene-based traits with species-wide variations.
Area of Science:
- Developmental Biology
- Evolutionary Biology
- Genetics
Background:
- Model organisms offer limited insights into the full spectrum of phenotypic diversity.
- Understanding natural phenotypic variation is crucial for advancing developmental and genetic research.
- The Phenoscape Knowledgebase (KB) was developed to explore and discover phenotypic variations across species.
Purpose of the Study:
- To demonstrate the utility of the Phenoscape KB in identifying evolutionary phenotypes.
- To enable comparisons between phenotypes from genetic perturbations in model organisms and evolutionary phenotypes.
- To facilitate the discovery of taxa exhibiting evolutionary variation similar to query genes.
Main Methods:
- Phenotypes in the KB are annotated using standardized ontologies for consistent comparison.
- An evolutionary profile, defined as variable phenotypes among daughter taxa, was created for each node in the taxonomic tree.
- Semantic similarity searches were performed to match gene-based phenotypes with evolutionary profiles, assessing statistical significance.
Main Results:
- The KB successfully identified taxa with evolutionary phenotypes mirroring those of query genes.
- The semantic similarity interface allows users to evaluate the statistical significance of matches.
- The system flags potential matches arising from differential annotation coverage between genetic and evolutionary studies.
Conclusions:
- The Phenoscape KB is a valuable tool for bridging genetic knowledge from model organisms with natural phenotypic diversity.
- This approach enhances our understanding of evolutionary phenotypes and their genetic underpinnings.
- The KB supports the challenge of integrating vast genetic data with the complexity of phenotypes observed in nature.
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