title: OryzaExpress: an integrated database of gene expression networks and omics annotations in rice.
abstract: Similarity of gene expression profiles provides important clues for understanding the biological functions of genes, biological processes and metabolic pathways related to genes. A gene expression network (GEN) is an ideal choice to grasp such expression profile similarities among genes simultaneously. For GEN construction, the Pearson correlation coefficient (PCC) has been widely used as an index to evaluate the similarities of expression profiles for gene pairs. However, calculation of PCCs for all gene pairs requires large amounts of both time and computer resources. Based on correspondence analysis, we developed a new method for GEN construction, which takes minimal time even for large-scale expression data with general computational circumstances. Moreover, our method requires no prior parameters to remove sample redundancies in the data set. Using the new method, we constructed rice GENs from large-scale microarray data stored in a public database. We then collected and integrated various principal rice omics annotations in public and distinct databases. The integrated information contains annotations of genome, transcriptome and metabolic pathways. We thus developed the integrated database OryzaExpress for browsing GENs with an interactive and graphical viewer and principal omics annotations (http://riceball.lab.nig.ac.jp/oryzaexpress/). With integration of Arabidopsis GEN data from ATTED-II, OryzaExpress also allows us to compare GENs between rice and Arabidopsis. Thus, OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology.
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Hamada
authors.forename: Kohei
authors.initials: K
authors.lastname: Hongo
authors.forename: Keita
authors.initials: K
authors.lastname: Suwabe
authors.forename: Akifumi
authors.initials: A
authors.lastname: Shimizu
authors.forename: Taishi
authors.initials: T
authors.lastname: Nagayama
authors.forename: Reina
authors.initials: R
authors.lastname: Abe
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Kikuchi
authors.forename: Naoki
authors.initials: N
authors.lastname: Yamamoto
authors.forename: Takaaki
authors.initials: T
authors.lastname: Fujii
authors.forename: Koji
authors.initials: K
authors.lastname: Yokoyama
authors.forename: Hiroko
authors.initials: H
authors.lastname: Tsuchida
authors.forename: Kazumi
authors.initials: K
authors.lastname: Sano
authors.forename: Takako
authors.initials: T
authors.lastname: Mochizuki
authors.forename: Nobuhiko
authors.initials: N
authors.lastname: Oki
authors.forename: Youko
authors.initials: Y
authors.lastname: Horiuchi
authors.forename: Masahiro
authors.initials: M
authors.lastname: Fujita
authors.forename: Masao
authors.initials: M
authors.lastname: Watanabe
authors.forename: Makoto
authors.initials: M
authors.lastname: Matsuoka
authors.forename: Nori
authors.initials: N
authors.lastname: Kurata
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics*; D014584:User-Computer Interface