AtGenExpress JPN
Last update:1/19/2009
DataContributed by AtGenExpressJAPAN Contributors Links

AtGenExpress is a multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. This large collaborative project will combine resources of gene expression patterns using Affymetrix GeneChip across the whole plant-life cycle.
    Sequencing of the Arabidopsis genome (The Arabidopsis Genome Initiative, 2000) was completed in 2000. It was the first step to understand the function of the genome. Genomeic sequencing and the collection of large numbers of cDNAs enabled to predict genome-wide genetic structure and to design DNA microarrays to monitor genome-wide gene expression. The Affymetrix ATH1 array, an oligonucleotide-based DNA microarray consisting of 22,746 probe sets, covering about 23,700 genes and nearly the entire genome of Arabidopsis, was designed based on computer-predicted genes (Redman et al., 2004). The system was widely accepted by the plant science community because of its high sensitivity and reproducibility. Using this system, an international research effort, the AtGenExpress consortium was organized to make an important contribution to science community and to add to our knowledge of gene functions in Arabidopsis. Large-scale transcriptome data sets developed by AtGenExpress consortium detailing the developmental process (Schmid et al., 2005) and stress responses (Kilian et al., 2007) in Arabidopsis have been reported. In this Web site, we present a hormone-response data set, representing treatment with phytohormones, hormone-inhibitors, hormone-related inhibitors, hormone-related mutants, seed germination processes and sulfate starvation (Goda et al., 2008).
    Redman, JC, Haas BJ, Tanimoto G, Town CD. (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant Journal 38: 545-561
    Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics 37: 501-506
    Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant Journal 50: 347-363
    Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi u, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y (2008) The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data access. Plant Journal 130: 1319-1334
The official data release Web site.
Web-based coexpression/expression viewer, ClusterCutting.
AtGenExpress data downloader (Japanese only)
Faster version of ClusterCutting (The system supports IE6 for windows users or Safari3 for Mac users.)
Data table of AtGenExpress Japan

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This site is managed Y.Shimada, E.Sasaki and C.Takahashi at.