Open Access Research article

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

Papapit Ingkasuwan1, Supatcharee Netrphan2, Sukon Prasitwattanaseree3, Morakot Tanticharoen1, Sakarindr Bhumiratana1, Asawin Meechai4, Jeerayut Chaijaruwanich5, Hideki Takahashi67 and Supapon Cheevadhanarak1*

Author Affiliations

1 School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, 10140, Thailand

2 National Center for Genetic Engineering and Biotechnology, Pathumthani, 12120, Thailand

3 Department of Statistics, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand

4 Department of Chemical Engineering, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, 10140, Thailand

5 Department of Computer Science, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand

6 RIKEN Plant Science Center, Yokohama, 230-0045, Japan

7 Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI, 48824, USA

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BMC Systems Biology 2012, 6:100  doi:10.1186/1752-0509-6-100

Published: 16 August 2012

Additional files

Additional file 1:

Figure S1. The gene association network of 11 carbon-related metabolisms inferred from GGM (Q < 0.05).

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Additional file 2:

Table S1. Genes in the starch sub-network.

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Additional file 3:

Table S2. Prediction of TF binding sites in 12 starch metabolic genes (2 kb-upstream).

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Additional file 4:

Figure S2. Expression patterns of 2 TFs, At3g07650 (COL9) and At1g05805 (bHLH), and their target genes.

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Additional file 5:

Figure S3. Expression patterns of starch genes in other regulatory modules.

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Additional file 6:

Figure S4. Expression pattern of C2H2 gene in the wild type, Atidd5, and col mutants quantified by qRT-PCR.

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Additional file 7:

Table S3. Descriptive statistics of chloroplast morphology, starch granule morphology, and starch granule number in the wild type, Atidd5, and col mutants.

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Additional file 8:

Table S4. T-DNA insertion lines of 6 candidate TFs that were utilized in this experiment.

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Additional file 9:

Table S5. Primer pairs for quantitative RT-PCR.

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