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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
The rice kinase database. A phylogenomic database for the rice kinome
Christopher Dardick1, Johann Chen, Todd Richter
1United States Department of Agriculture-Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, West Virginia 25430, USA.
Plant Physiology
|December 19, 2006
Summary
Researchers developed a database to explore the functions of rice protein kinases. This resource aids in understanding the vast majority of these important genes with unknown roles.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The rice (Oryza sativa) genome encodes 1,429 protein kinases.
- The functions of most rice protein kinases remain largely uncharacterized.
- Understanding these kinases is crucial for plant biology and agriculture.
Purpose of the Study:
- To create a centralized, user-friendly resource for the functional analysis of rice protein kinases.
- To facilitate comparative genomics and functional studies within the rice kinase gene family.
Main Methods:
- Development of a phylogenomic database (http://rkd.ucdavis.edu) integrating diverse biological data.
- Incorporation of sequence data, gene expression profiles, and protein-protein interaction maps.
- Utilizing phylogenetic trees and interactive interfaces for data visualization and exploration.
- Integration with Cytoscape for visualizing protein-protein interaction networks.
Main Results:
- The database provides a platform for displaying kinase data within a phylogenetic context.
- Comparative analysis of kinase subfamilies is enabled through the integrated data.
- Interactive exploration of chromosomal distribution for all rice kinases is available.
- Protein-protein interaction maps are accessible and visualized using Cytoscape.
Conclusions:
- The created phylogenomic database serves as a valuable tool for investigating rice kinase functions.
- This resource facilitates deeper understanding of the rice kinome and its biological roles.
- The database supports future research in plant kinase biology and functional genomics.
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