title: The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.
abstract: We analyzed global gene expression in Arabidopsis in response to various hormones and in related experiments as part of the AtGenExpress project. The experimental agents included seven basic phytohormones (auxin, cytokinin, gibberellin, brassinosteroid, abscisic acid, jasmonate and ethylene) and their inhibitors. In addition, gene expression was investigated in hormone-related mutants and during seed germination and sulfate starvation. Hormone-inducible genes were identified from the hormone response data. The effects of each hormone and the relevance of the gene lists were verified by comparing expression profiles for the hormone treatments and related experiments using Pearson's correlation coefficient. This approach was also used to analyze the relationships among expression profiles for hormone responses and those included in the AtGenExpress stress-response data set. The expected correlations were observed, indicating that this approach is useful to monitor the hormonal status in the stress-related samples. Global interactions among hormones-inducible genes were analyzed in a pairwise fashion, and several known and novel hormone interactions were detected. Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that our data set is useful for identification of clusters of co-expressed genes, and to predict the functions of unknown genes, even if a gene's function is not directly related to the experiments included in AtGenExpress. Our data are available online from AtGenExpressJapan; the results of genome-wide HCA are available from PRIMe. The data set presented here will be a versatile resource for future hormone studies, and constitutes a reference for genome-wide gene expression in Arabidopsis.
authors.affiliation: RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Goda
authors.forename: Eriko
authors.initials: E
authors.lastname: Sasaki
authors.forename: Kenji
authors.initials: K
authors.lastname: Akiyama
authors.forename: Akiko
authors.initials: A
authors.lastname: Maruyama-Nakashita
authors.forename: Kazumi
authors.initials: K
authors.lastname: Nakabayashi
authors.forename: Weiqiang
authors.initials: W
authors.lastname: Li
authors.forename: Mikihiro
authors.initials: M
authors.lastname: Ogawa
authors.forename: Yukika
authors.initials: Y
authors.lastname: Yamauchi
authors.forename: Jeremy
authors.initials: J
authors.lastname: Preston
authors.forename: Ko
authors.initials: K
authors.lastname: Aoki
authors.forename: Takatoshi
authors.initials: T
authors.lastname: Kiba
authors.forename: Suguru
authors.initials: S
authors.lastname: Takatsuto
authors.forename: Shozo
authors.initials: S
authors.lastname: Fujioka
authors.forename: Tadao
authors.initials: T
authors.lastname: Asami
authors.forename: Takeshi
authors.initials: T
authors.lastname: Nakano
authors.forename: Hisashi
authors.initials: H
authors.lastname: Kato
authors.forename: Takeshi
authors.initials: T
authors.lastname: Mizuno
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Sakakibara
authors.forename: Shinjiro
authors.initials: S
authors.lastname: Yamaguchi
authors.forename: Eiji
authors.initials: E
authors.lastname: Nambara
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kamiya
authors.forename: Hideki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Masami Yokota
authors.initials: MY
authors.lastname: Hirai
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.forename: Shigeo
authors.initials: S
authors.lastname: Yoshida
authors.forename: Yukihisa
authors.initials: Y
authors.lastname: Shimada
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D016000:Cluster Analysis; D030541:Databases, Genetic; D015870:Gene Expression / Q000187:drug effects*; D020869:Gene Expression Profiling; D018745:Genome, Plant; D005838:Genotype; D010937:Plant Growth Regulators / Q000037:antagonists & inhibitors / Q000494:pharmacology*; D012639:Seeds / Q000187:drug effects / Q000235:genetics / Q000254:growth & development
chemical_list: D010937:Plant Growth Regulators