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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



Deciphering the metabolome is essential for a better understanding of the cellular metabolism as a system. Typical metabolomics data show a few but significant correlations among metabolite levels when data sampling is repeated across individuals grown under strictly controlled conditions. Although several studies have assessed topologies in metabolomic correlation networks, it remains unclear whether highly connected metabolites in these networks have specific functions in known tissue- and/or genotype-dependent biochemical pathways.


In our study of metabolite profiles we subjected root tissues to gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) and used published information on the aerial parts of 3 Arabidopsis genotypes, Col-0 wild-type, methionine over-accumulation 1 (mto1), and transparent testa4 (tt4) to compare systematically the metabolomic correlations in samples of roots and aerial parts. We then applied graph clustering to the constructed correlation networks to extract densely connected metabolites and evaluated the clusters by biochemical-pathway enrichment analysis. We found that the number of significant correlations varied by tissue and genotype and that the obtained clusters were significantly enriched for metabolites included in biochemical pathways.


We demonstrate that the graph-clustering approach identifies tissue- and/or genotype-dependent metabolomic clusters related to the biochemical pathway. Metabolomic correlations complement information about changes in mean metabolite levels and may help to elucidate the organization of metabolically functional modules.