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BIOINFORMATICS

The Rice Kinase Database. A Phylogenomic Database for the Rice Kinome^1,[OA]

United States Department of Agriculture-Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, West Virginia, 25430 (C.D.); Department of Plant Pathology, University of California, Davis, California, 95616 (J.C., T.R., P.R.); and Institute for Genomic Research, Rockville, Maryland, 20853 (S.O.)

The rice (Oryza sativa) genome contains 1,429 protein kinases, the vast majority of which have unknown functions. We created a phylogenomic database (http://rkd.ucdavis.edu) to facilitate functional analysis of this large gene family. Sequence and genomic data, including gene expression data and protein-protein interaction maps, can be displayed for each selected kinase in the context of a phylogenetic tree allowing for comparative analysis both within and between large kinase subfamilies. Interaction maps are easily accessed through links and displayed using Cytoscape, an open source software platform. Chromosomal distribution of all rice kinases can also be explored via an interactive interface.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Pamela C. Ronald (pcronald{at}ucdavis.edu).

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.087270

^* Corresponding author; e-mail pcronald{at}ucdavis.edu; fax 530–752–5674.

Received July 24, 2006; accepted November 17, 2006; published December 15, 2006.

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