The AtGenExpress hormone and chemical treatment data set: Experimental design, data evaluation, model data analysis and data access

Hideki Goda, Eriko Sasaki, Kenji Akiyama, Akiko Maruyama-Nakashita, Kazumi Nakabayashi, Weiqiang Li, Mikihiro Ogawa, Yukika Yamauchi, Jeremy Preston, Ko Aoki, Takatoshi Kiba, Suguru Takatsuto, Shozo Fujioka, Tadao Asami, Takeshi Nakano, Hisashi Kato, Takeshi Mizuno, Hitoshi Sakakibara, Shinjiro Yamaguchi, Eiji NambaraYuji Kamiya, Hideki Takahashi, Masami Yokota Hirai, Tetsuya Sakurai, Kazuo Shinozaki, Kazuki Saito, Shigeo Yoshida, Yukihisa Shimada

    Research output: Contribution to journalArticle

    339 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)526-542
    Number of pages17
    JournalPlant Journal
    Volume55
    Issue number3
    DOIs
    Publication statusPublished - 2008 Aug 1

    Keywords

    • AtGenExpress
    • Chemical genomics
    • Co-expression network analysis
    • Phytohormone network analysis
    • Systems biology

    ASJC Scopus subject areas

    • Genetics
    • Plant Science
    • Cell Biology

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  • Cite this

    Goda, H., Sasaki, E., Akiyama, K., Maruyama-Nakashita, A., Nakabayashi, K., Li, W., Ogawa, M., Yamauchi, Y., Preston, J., Aoki, K., Kiba, T., Takatsuto, S., Fujioka, S., Asami, T., Nakano, T., Kato, H., Mizuno, T., Sakakibara, H., Yamaguchi, S., ... Shimada, Y. (2008). The AtGenExpress hormone and chemical treatment data set: Experimental design, data evaluation, model data analysis and data access. Plant Journal, 55(3), 526-542. https://doi.org/10.1111/j.1365-313X.2008.03510.x