title: Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza Sativa and Other Plant Species.
abstract: Analysis of a gene expression network (GEN), which is constructed based on similarity of gene expression profiles, is a widely used approach to gain clues for new biological insights. The recent abundant availability of transcriptome data in public databases is enabling GEN analysis under various experimental conditions, and even comparative GEN analysis across species. To provide a platform to gain biological insights from public transcriptome data, valuable databases have been created and maintained. This chapter introduces the web database OryzaExpress, providing omics information on Oryza sativa (rice). The integrated database Plant Omics Data Center, supporting a wide variety of plant species, is also described to compare omics information among multiple plant species.
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Kudo
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
authors.forename: Shin
authors.initials: S
authors.lastname: Terashima
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
authors.forename: Yuno
authors.initials: Y
authors.lastname: Takaki
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
authors.forename: Yukino
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan. kyano@isc.meiji.ac.jp.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D012275:Oryza / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D059467:Transcriptome; D064878:Web Browser
keywords: Correspondence analysis; Gene expression network; Microarray; Ortholog; Plant; RNA-seq; Transcriptome