RRC ID 25690
著者 Sato Y, Namiki N, Takehisa H, Kamatsuki K, Minami H, Ikawa H, Ohyanagi H, Sugimoto K, Itoh J, Antonio BA, Nagamura Y.
タイトル RiceFREND: a platform for retrieving coexpressed gene networks in rice.
ジャーナル Nucleic Acids Res
Abstract Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs and tissues at different developmental stages, mature organs throughout the growth from transplanting until harvesting in the field and plant hormone treatment conditions, using a single microarray platform. The database is provided with two search options, namely, 'single guide gene search' and 'multiple guide gene search' to efficiently retrieve information on coexpressed genes. A user-friendly web interface facilitates visualization and interpretation of gene coexpression networks in HyperTree, Cytoscape Web and Graphviz formats. In addition, analysis tools for identification of enriched Gene Ontology terms and cis-elements provide clue for better prediction of biological functions associated with the coexpressed genes. These features allow users to clarify gene functions and gene regulatory networks that could lead to a more thorough understanding of many complex agronomic traits.
巻・号 41(Database issue)
ページ D1214-21
公開日 2013-1-1
DOI 10.1093/nar/gks1122
PII gks1122
PMID 23180784
PMC PMC3531108
MeSH Databases, Genetic* Gene Expression Profiling* Gene Regulatory Networks* Genes, Plant* Internet Molecular Sequence Annotation Oryza / genetics* Oryza / growth & development Oryza / metabolism Plant Proteins / genetics Plant Proteins / metabolism Software
IF 11.502
引用数 60
WOS 分野 BIOCHEMISTRY & MOLECULAR BIOLOGY
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