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Open Access Highly Accessed Research article

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach

Atsushi Fukushima1, Miyako Kusano12, Henning Redestig1, Masanori Arita134 and Kazuki Saito15*

Author Affiliations

1 RIKEN Plant Science Center, Kanagawa 230-0045, Japan

2 Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan

3 The University of Tokyo, Tokyo 113-0033, Japan

4 Keio University, Yamagata 997-0052, Japan

5 Chiba University, Chiba 263-8522, Japan

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BMC Systems Biology 2011, 5:1  doi:10.1186/1752-0509-5-1

Published: 1 January 2011

Additional files

Additional file 1:

Raw data matrix used in this study. The normalized data matrix of 166 peak areas of extracted mass spectra for 53 root samples (17 × WT, 16 × mto1, and 20 × tt4; see also Methods).

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Additional file 2:

Discriminative metabolites of PCA loadings and significant changes in the metabolite levels of WT, mto1, and tt4. All 59 metabolites that contributed to the separation of the mutant profiles group from WT are shown: mto1/WT in the roots (A) and aerial parts (B) and tt4/WT in the roots (C) and aerial parts (D). Differentially changed metabolites were identified with the rank product method (see Methods). Significantly changed metabolites manifested a false discovery rate (FDR) < 0.05.

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Additional file 3:

PCA by removing four metabolites (methionine, urea, glycine, and pipecolate) in (A) roots and (B) aerial parts using datasets including 55 metabolites. See also the legend to Figure 2.

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Additional file 4:

List of metabolomic correlations based on Spearman's coefficient for the aerial parts and roots of WT, mto1, and tt4. r1 and r2 represent the coefficient of WT and the mutant, respectively. p1 and p2 are the p-value of the correlation test for WT and the mutant, respectively. 'p (diff)' is the p-value of comparing correlations using Fisher Z-transformation. (r1 - r2) is the subtraction of r2 from r1. 'fdr' is the local false discovery rate (fdr)-controlled p-value using the 'fdrtool' package [29].

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Additional file 5:

Correlation network properties of the 59 metabolites in the aerial parts across a range of correlation coefficients. Networks were constructed for a range of correlation thresholds from 0 to 1.0 by 0.01 increments, and each resulting network was calculated for: (A) the graph density - the ratio of the number of edges and the number of possible edges, (B) the clustering coefficient, (C) the average degree of all nodes, (D) the average path length, (E) the number of connected components, and (F) the number of metabolite-metabolite correlations (edges) in the network. Within each plot, black solid circles represent the observed data points; black dots represent 100 randomized data. This calculation was performed to generate a null distribution.

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Additional file 6:

Correlation network properties of the 59 metabolites in roots across a range of correlation coefficients. See details in the legend for Additional file 5.

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Additional file 7:

Resulting clusters detected by the DPClus algorithm. For details, see the manual of DPClus http://kanaya.naist.jp/DPClus/ webcite.

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Additional file 8:

Visualization of all DPClus clusters. See details in the legend for Figure 4.

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Additional file 9:

List of KEGG pathways used in this study.

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