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Plant and Cell Physiology Advance Access originally published online on January 23, 2007
Plant and Cell Physiology 2007 48(3):381-390; doi:10.1093/pcp/pcm013
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© The Author 2007. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

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Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology

Koh Aoki1, Yoshiyuki Ogata1 and Daisuke Shibata*

Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, 292-0818 Japan

*Corresponding author: E-mail, shibata{at}kazusa.or.jp; Fax, +81-438-52-3948.


  Abstract

Gene co-expression, in many cases, implies the presence of a functional linkage between genes. Co-expression analysis has uncovered gene regulatory mechanisms in model organisms such as Escherichia coli and yeast. Recently, accumulation of Arabidopsis microarray data has facilitated a genome-wide inspection of gene co-expression profiles in this model plant. An approach using network analysis has provided an intuitive way to represent complex co-expression patterns between many genes. Co-expression network analysis has enabled us to extract modules, or groups of tightly co-expressed genes, associated with biological processes. Furthermore, integrated analysis of gene expression and metabolite accumulation has allowed us to hypothesize the functions of genes associated with specific metabolic processes. Co-expression network analysis is a powerful approach for data-driven hypothesis construction and gene prioritization, and provides novel insights into the system-level understanding of plant cellular processes.

Keywords: Co-expression - Correlation - Metabolome - Network - Systems biology - Transcriptome

Abbreviations: CESA, cellulose synthase; CTL, endochitinase-like; EST, expressed sequence tag; MEP, methylerythritol phosphate; MVA, mevalonate; PCC, Pearson correlation coefficient.

1These authors contributed equally to this work.

(Received October 13, 2006; Accepted January 19, 2007)
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