Research article
Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress
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* Corresponding author: Benildo G de los Reyes benildo.de@maine.edu
- † Equal contributors
1 School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
2 South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
3 Crop Research Informatics Laboratory, International Rice Research Institute, Los Banos, Laguna, Philippines
4 Department of Chemical and Biomolecular Engineering, National University of Singapore, 117576, Singapore
5 Computational Biology Research Center, AIST Tokyo Waterfront, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan
6 Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
BMC Plant Biology 2010, 10:16 doi:10.1186/1471-2229-10-16
Published: 25 January 2010Additional files
Additional file 1:
Dominant functional categories in the downregulated group of genes. This data shows the most highly enriched broad functional categories of downregulated genes classified according to gene ontology.
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Additional file 2:
Expression matrix of chilling upregulated WRKY transcription factors. Heat map showing the temporal expression profiles of WRKY transcription factors under chilling stress. Gene designations were based on putative Arabidopsis orthologs according to the most recent genome annotation.
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Additional file 3:
Expression matrix of chilling upregulated bHLH transcription factors. Heat map showing the temporal expression profiles of bHLH transcription factors under chilling stress. Gene designations were based on putative Arabidopsis orthologs according to the most recent genome annotation.
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Additional file 4:
Expression matrix of chilling upregulated NAC transcription factors. Heat map showing the temporal expression profiles of NAC transcription factors under chilling stress. Gene designations were based on putative Arabidopsis orthologs according to the most recent genome annotation.
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Additional file 5:
Functional categories and grouping by cluster of chilling upregulated NTF genes. List of all NTF genes included in the analysis of the chilling upregulated transcriptome grouped according to putative functions.
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Additional file 6:
Correlation between timing of induction and function of chilling responsive genes. Distribution of functional categories in relation to activation timing of co-expressed gene clusters. (A) Signaling and response regulation; (B) cellular defense and rescue; (C) physiological adjustment and sustenance mechanisms. Gray: rapid phase-1 clusters; Red: phase-2 and phase-3 clusters.
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Additional file 7:
Relative enrichment of other types of cis-elements detected in the promoters of chilling upregulated genes. List of cis-elements associated with other types of transcription factors not included in Tables 2, 3 and 4.
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Additional file 8:
Components of the chilling stress transcriptome with possible roles in oxidative stress and redox regulation. List of upregulated genes with possible roles in oxidative stress and redox regulation classified according to gene ontology.
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Additional file 9:
Components of the chilling stress transcriptome with possible roles in response to diseases, elicitors and apoptosis. List of upregulated genes with possible roles in response to diseases, elicitors and apoptosis classified according to gene ontology.
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Additional file 10:
Components of the chilling stress transcriptome with possible roles in cellular detoxification and efflux. List of upregulated genes with possible roles in cellular detoxification and efflux classified according to gene ontology.
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Additional file 11:
Possible components of physiological adjustment and sustenance mechanisms. Functional categories relevant to physiological adjustment and sustenance processes classified according to gene ontology.
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Additional file 12:
Association between chilling-induced transcription factors and stress-associated QTL. Genomic location of chilling upregulated transcription factors relative to the boundaries of known QTL of rice associated with seedling vigor and stress response.
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