Approaches for extracting practical information from gene co-expression networks in plant biology

Plant Cell Physiol. 2007 Mar;48(3):381-90. doi: 10.1093/pcp/pcm013. Epub 2007 Jan 23.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Arabidopsis / genetics
  • Cell Wall / genetics
  • Cell Wall / metabolism
  • Databases, Genetic
  • Gene Expression Regulation, Plant
  • Genome, Plant
  • Genomics
  • Oligonucleotide Array Sequence Analysis
  • Plants / genetics*
  • Plants / metabolism
  • Systems Biology
  • Terpenes / metabolism


  • Terpenes