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

• Published in: Plant and cell physiology Vol. 48; no. 3; pp. 381 - 390
• Main Authors: Aoki, Koh, Ogata, Yoshiyuki, Shibata, Daisuke
• Format: Journal Article
• Language: English
• Published: Japan Oxford University Press 01.03.2007; Oxford Publishing Limited (England)
• Subjects: Arabidopsis; Arabidopsis - genetics; Cell Wall - genetics; Cell Wall - metabolism; Databases, Genetic; Escherichia coli; Gene Expression Regulation, Plant; Genome, Plant; Genomics; Oligonucleotide Array Sequence Analysis; Plants - genetics; Plants - metabolism; Systems Biology; Terpenes - metabolism; Metabolome; Co-expression; Correlation; Systems biology; Network; Transcriptome
• ISSN: 0032-0781; 1471-9053
• DOI: 10.1093/pcp/pcm013

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.