title: RiceFREND: a platform for retrieving coexpressed gene networks in rice.
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.
authors.affiliation: Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Sato
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.forename: Hinako
authors.initials: H
authors.lastname: Takehisa
authors.forename: Kaori
authors.initials: K
authors.lastname: Kamatsuki
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Minami
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ikawa
authors.forename: Hajime
authors.initials: H
authors.lastname: Ohyanagi
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Sugimoto
authors.forename: Jun-Ichi
authors.initials: J
authors.lastname: Itoh
authors.forename: Baltazar A
authors.initials: BA
authors.lastname: Antonio
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D020407:Internet; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D010940:Plant Proteins