Open Access Highly Accessed Research article

Characterization of WRKY co-regulatory networks in rice and Arabidopsis

Stefano Berri12, Pamela Abbruscato3, Odile Faivre-Rampant34, Ana CM Brasileiro56, Irene Fumasoni3, Kouji Satoh7, Shoshi Kikuchi7, Luca Mizzi1, Piero Morandini8, Mario Enrico Pè19 and Pietro Piffanelli3*

Author Affiliations

1 Department of Biomolecular Sciences and Biotechnology, University of Milan, via Celoria 26, 20133 Milan, Italy

2 School of Computing, University of Leeds, LS2 9JT Leeds, UK

3 Rice Genomics Unit, Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy

4 UMR BGPI, CIRAD, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France

5 Parque Estação Biológica, Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte, 02372, Brasília DF, Brazil

6 UMR DAP, CIRAD, Avenue Agropolis, 34398 Montpellier Cedex 5, France

7 Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan

8 Department of Biology, University of Milan and CNR Institut of Biophysics (Milan Section), via Celoria 26, 20133 Milan, Italy

9 Sant'Anna School for Advanced Studies, Piazza Martiri della Libertà 33, 56127 Pisa, Italy

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BMC Plant Biology 2009, 9:120  doi:10.1186/1471-2229-9-120

Published: 22 September 2009

Additional files

Additional file 1:

OsWRKY gene list. List of the retrieved 104 OsWRKY genes with their corresponding gene names used in this article together with their ID used for the OsWRKYARRAY microarray analysis. Gene locus in TIGR nomenclature (release 5) and names provided in earlier publications are reported.

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Additional file 2:

Arabidopsis - rice WRKY phylogenetic tree. Phylogenetic tree of rice and Arabidopsis WRKY domains obtained with the Maximum Likelihood method using PHYML [68]. Both the N and the C WRKY domains were considered for those proteins bearing two domains. Bootstrap values higher than 50 are indicated on the nodes. The sequences of Giardia lamblia, Dictyostelium discoideum and Chlamydomonas reinhadrtii were included. The tree image was produced using iTOL software [69]. The three distinct sub-groups of group 3 identified in this study are indicated as 3A, 3B and 3C.

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Additional file 3:

OsWRKY microarray oligonucleotides. List of the set of oligonucleotides used for the OsWRKYARRAY microarray together with their ID and sequences.

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Additional file 4:

AtWRKY genes scatter plots. Typical scatter plot of the expression level of two pairs of AtWRKY genes across the set of Arabidopsis microarray experiments used for the Pearson Correlation Coefficient analysis. Each grey dot represents the simultaneous expression level of the two genes in one microarray experiment. A: The expression level of AtWRKY40 is not correlated with the expression of AtWRKY35. B: A strong correlation is present between AtWRKY40 and AtWRKY33.

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Additional file 5:

Linear Pearson Correlation Matrix of AtWRKY genes. Correlation matrix of the untransformed Pearson Correlation Coefficient (PCC) values of the set of AtWRKY genes under examination.

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Additional file 6:

Logarithmic Pearson Correlation Matrix of AtWRKY genes. Correlation matrix of the logarithmic-transformed Pearson Correlation Coefficient (PCC) values of the set of AtWRKY genes under examination.

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Additional file 7:

Plot of edges and mean of edges/gene vs PCC threshold value. Plots of the number of edges (Y axis on the left) and mean of edges/gene (Y axis on the right) as a function of the PCC threshold values in the linear Pearson Correlation Coefficient analysis (P-lin) of the Arabidopsis MADS-BOX (above) and WRKY (below) genes.

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Additional file 8:

Plot of edges and number of genes vs PCC threshold value. Plots of the number of edges and number of genes as a function of the PCC threshold values in the P-lin linear (above) and log-transformed (below) Pearson Correlation Coefficient analysis of the Arabidopsis WRKY (AtWRKY) genes.

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Additional file 9:

P-lin co-regulatory networks of Arabidopsis MADS-BOX genes. Co-regulatory networks of Arabidopsis MADS-BOX genes obtained using untransformed Pearson Correlation Coefficient analysis (P-lin analysis). A: PCC threshold value of 0.6 B: PCC threshold value of 0.7. Unbroken lines indicate experimentally validated edges reported in literature; broken lines indicate edges not yet experimentally validated. The thickness of the edges is proportional to the value of the Pearson Coefficient. Thick black line: Pearson Correlation Coefficient 0.96; Thin Black Line: Pearson Correlation Coefficient 0.6 (in panel A) and 0.7 (in Panel B); the proximity of two genes on the graph is not indicative of their relatedness.

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Additional file 10:

P-log co-regulatory networks of Arabidopsis MADS-BOX genes. Co-regulatory networks of Arabidopsis MADS-BOX genes obtained using log-transformed Pearson Correlation Coefficient analysis (P-log analysis). A: PCC threshold value of 0.6 B: PCC threshold value of 0.7. Unbroken lines indicate experimentally validated edges reported in literature; broken lines indicate edges not yet experimentally validated. The thickness of the edges is proportional to the value of the Pearson Coefficient. Thick black line: Pearson Correlation Coefficient 0.96; Thin Black Line: Pearson Correlation Coefficient 0.6 (in panel A) and 0.7 (in Panel B); the proximity of two genes on the graph is not indicative of their relatedness.

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Additional file 11:

List of Arabidopsis WRKY genes present in the co-regulatory. List of the Arabidopsis WRKY genes with their affiliation to the different co-regulatory networks according to the P-lin and P-log Correlation analysis (see Figure 4) and their assigned phylogenetic group (see Additional file 2).

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Additional file 12:

Co-regulatory networks of Arabidopsis WRKY genes. Co-regulatory networks of Arabidopsis WRKY genes obtained with the PCC threshold value of 0.7 in the untransformed (P-lin) (panel A) and log transformed (P-log) Pearson Correlation Coefficient analysis (panel B). The thickness of the edges is proportional to the value of the Pearson Correlation Coefficient. Thick black line: Pearson Correlation Coefficient 0.96; Thin Black Line: Pearson Correlation Coefficient 0.7. The proximity of two genes on the graph is not indicative of their relatedness.

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Additional file 13:

OsWRKY primer sequences used for quantitative RT-PCR analysis. The sequences of primers used to analyse the expression levels of 14 OsWRKY genes by quantitative RT-PCR analysis are listed.

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