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PMID: 17172291 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

The rice kinase database. A phylogenomic database for the rice kinome.

Plant physiology ·Vol. 143 ·No. 2 ·2007-02-00 ·Pages 579-86

Dardick C, Chen J, Richter T, Ouyang S, Ronald P

Abstract

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.

MeSH Terms
Amino Acid Motifs Base Sequence Chromosome Mapping Chromosomes, Plant DNA Transposable Elements/genetics DNA, Plant Databases, Factual Genome, Plant Molecular Sequence Data Mutagenesis, Insertional Oryza/classification,enzymology,genetics Phosphotransferases/genetics,metabolism Phylogeny Protein Binding
Chemicals
DNA Transposable Elements DNA, Plant Phosphotransferases
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Dardick Christopher
United States Department of Agriculture-Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, West Virginia 25430, USA.
Chen Johann
Richter Todd
Ouyang Shu
Ronald Pamela
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.106.087270
Published
2007-02-00
Epub
2006-00-15
Pages
579-86
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC1803753
Subset
IM
Grants
NIGMS NIH HHS · GM59962 · United States
NIGMS NIH HHS · K12GM00679 · United States
External Links
PubMed source DOI: 10.1104/pp.106.087270 PMC Full Text View journal details
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