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

@article{Goda2008TheAH,
  title={The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.},
  author={Hideki Goda and Eriko Sasaki and Kenji Akiyama and Akiko Maruyama-Nakashita and Kazumi Nakabayashi and Weiqiang Li and Mikihiro Ogawa and Yukika Yamauchi and Jeremy Preston and Koh Aoki and Takatoshi Kiba and Suguru Takatsuto and Shozo Fujioka and Tadao Asami and Takeshi Nakano and Hisashi Kato and Takeshi Mizuno and Hitoshi Sakakibara and Shinjiro Yamaguchi and Eiji Nambara and Yuji Kamiya and Hideki Takahashi and Masami Yokota Hirai and Tetsuya Sakurai and Kazuo Shinozaki and Kazuki Saito and Shigeo Yoshida and Yukihisa Shimada},
  journal={The Plant journal : for cell and molecular biology},
  year={2008},
  volume={55 3},
  pages={
          526-42
        }
}
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… 
View on PubMed
hos.ufl.edu
207 Citations
Highly Influential Citations
16
Background Citations
71
Methods Citations
46
Results Citations
8

Figures and Tables from this paper

207 Citations

Citation Type

Citation Type

Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon
TLDR
A comprehensive analysis of hormone-regulated genes in Brachypodium distachyon using RNA sequencing technology provides information useful to understand the diversity and similarity of hormones-regulated transcriptional responses between eudicots and monocots.
HORMONOMETER: A Tool for Discerning Transcript Signatures of Hormone Action in the Arabidopsis Transcriptome1[W][OA]
TLDR
A vector-based algorithm that rapidly compares lists of transcripts yielding correlation values is developed and provides a diagnostic tool for evaluating the physiological state of being of the plant from the point of view of transcripts regulated by hormones and yields biological insight into the multiple response components that enable plant adaptation to the environment.
Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice
TLDR
This study investigated the exogenous effect of plant hormones, including auxin, cytokinin, abscisic acid, ethylene, salicylic acid and jasmonic Acid, on the transcription of rice genes at whole genome level using microarray to identify genes involved in several biological processes whose expression was altered significantly in the presence of different hormones.
UniVIO: A Multiple Omics Database with Hormonome and Transcriptome Data from Rice
TLDR
A database named Uniformed Viewer for Integrated Omics, which displays hormone-metabolome (hormonome) and transcriptome data in a single formatted (uniformed) heat map, and a correlation search function has been implemented to enable users to obtain information of correlated substance accumulation and gene expression.
Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening
TLDR
A transcriptome analysis combined with the evaluation of sucrose metabolism and hormone profiling of sugarcane plants sprayed with ethephon or aminoethoxyvinylglycine (AVG), an ethylene inhibitor, at the onset of ripening identified potential ethylene target genes and characterized the hormonal status during ripening, providing insights into the action of ethylene at the site of Sucrose accumulation.
Microarray Analysis of Transcriptional Responses to Abscisic Acid and Salt Stress in Arabidopsis thaliana
TLDR
Gene ontology (GO) analysis revealed four subgroups of genes, including genes in the GO categories “Molecular transducer activity’, “Growth”, ”Biological adhesion” and “Pigmentation” which were expressed in response to ABA stress but not NaCl stress, which may help elucidate differences in the response of plants to salt and ABA Stress.
Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
TLDR
The authors' prediction of Arabidopsis cis-regulatory elements for phytohormone responses provides guidance for experimental analysis of promoters to reveal the basis of the transcriptional network of phyt ohormones.
Transcriptome analysis uncovers Arabidopsis F-BOX STRESS INDUCED 1 as a regulator of jasmonic acid and abscisic acid stress gene expression
TLDR
FBS1 impacts plant stress responses by regulating hundreds of genes that respond to the plant stress hormones JA and ABA, and is concluded that it might have a role in tuning hormone responses to particular circumstances at the transcriptional level.
Stability of housekeeping gene expression in Arabidopsis thaliana seedlings under differing macronutrient and hormonal conditions
TLDR
The expression stability of housekeeping genes in cytokinin series was studied in wide spectrum of plants treated with different adenine- and phenylurea-type cytokinins as well as in plants with controlled overexpression of agrobacterial isopentenyltransferase.
Architecture and dynamics of the jasmonic acid gene regulatory network
TLDR
High-resolution RNA-Seq time series analyses of methyl JA-treated Arabidopsis thaliana revealed several transcription factors that were uncovered as early components of the JA gene regulatory network with a role in pathogen and insect resistance.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 70 REFERENCES
The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.
TLDR
The results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
Gibberellin Biosynthesis and Response during Arabidopsis Seed Germination Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011650.
TLDR
In situ hybridization analysis demonstrated that the expression of GA-responsive genes is not restricted to the predicted site of GA biosynthesis, suggesting that GA itself, or GA signals, is transmitted across different cell types during Arabidopsis seed germination.
The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affects auxin response in Arabidopsis.
TLDR
Findings suggest that HAT2 plays opposite roles in the shoot and root tissues in regulating auxin-mediated morphogenesis, suggesting that auxin signals are mediated by a master set of diverse transcriptional regulators.
Organ-Specific Expression of Brassinosteroid-Biosynthetic Genes and Distribution of Endogenous Brassinosteroids in Arabidopsis
TLDR
Findings indicate that BRs are synthesized in all organs tested, but are most actively synthesizing in young, actively developing organs, in contrast, synthesis was limited in mature organs.
Activation of Gibberellin Biosynthesis and Response Pathways by Low Temperature during Imbibition of Arabidopsis thaliana Seeds On-line version contains Web-only data.
TLDR
It is found that a subset of gibberellin biosynthesis genes were upregulated in response to low temperature, resulting in an increase in the level of bioactive GAs and transcript abundance of GA-inducible genes in imbibed Arabidopsis thaliana seeds.
Transcription of the Arabidopsis CPD gene, encoding a steroidogenic cytochrome P450, is negatively controlled by brassinosteroids.
TLDR
Repression of CPD transcription by brassinosteroids is sensitive to the protein synthesis inhibitor cycloheximide, indicating a requirement for de novo synthesis of a regulatory factor.
Characterisation of BRH1, a brassinosteroid-responsive RING-H2 gene from Arabidopsis thaliana
TLDR
Considering the potential of the RING proteins to participate in regulatory protein complexes, BR-dependent expression of BRH1 may suggest its involvement in later hormonal effects.
JASMONATE-INSENSITIVE1 Encodes a MYC Transcription Factor Essential to Discriminate between Different Jasmonate-Regulated Defense Responses in Arabidopsis
TLDR
The identification of several new loci involved in JA signaling and the characterization and positional cloning of one of them, JASMONATE-INSENSITIVE1 (JAI1/JIN1), a nuclear-localized basic helix-loop-helix-leucine zipper transcription factor whose expression is rapidly upregulated by JA, are described.
Arabidopsis Aux/IAA genes are involved in brassinosteroid-mediated growth responses in a manner dependent on organ type.
TLDR
The results suggest that Aux/IAA proteins function in auxin- and BR-signaling pathways, and that IAA proteins function as the signaling components modulating BR sensitivity in a manner dependent on organ type.
Combinatorial microarray analysis revealing arabidopsis genes implicated in cytokinin responses through the His->Asp Phosphorelay circuitry.
TLDR
The idea that certain genes encoding transcription factors are rapidly and specifically induced at the level of transcription by cytokinin in a manner similar to that of the type-A ARR genes is supported, which are the hallmarks of the His-->Asp phosphorelay signaling circuitry.
...
1
2
3
4
5
...