Journal Article

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

Koh Aoki, Yoshiyuki Ogata and Daisuke Shibata

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 48, issue 3, pages 381-390
Published in print March 2007 | ISSN: 0032-0781
Published online March 2007 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcm013
Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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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

Journal Article.  5254 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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