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

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.

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

“…Recently, expression data, functional gene annotations, protein-protein interaction data, knockout phenotype information, and cis-regulatory elements have been combined to delineate coexpressed modules, to predict new gene functions, and to identify transcriptional regulatory interactions (Aoki et al, 2007;Vandepoele et al, 2009;De Bodt et al, 2010;Mutwil et al, 2010;Obayashi and Kinoshita, 2010). Although most coexpression approaches have been used to predict different types of gene-gene interactions in model species such as Arabidopsis and rice, interspecies comparisons have identified examples of conserved coexpression modules in plants (Ma et al, 2005;Street et al, 2008).…”

A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity

“…In Escherichia coli, yeast, and animals, coexpression analysis is an established tool to predict functional networks (24,25), and sophisticated software tools have been especially developed for this purpose (26). Although this approach has also been suggested as a tool for the identification of linked gene functions in plants (27), few studies have addressed this method experimentally in this taxonomic group of organisms (28)(29)(30)(31). In the …”

Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene–Metabolite Correlations inArabidopsis

“…The coexpression relationships of all Arabidopsis genes exhibiting correlation coefficients > 0.525 (r > 0.525, all data sets version 3) with the query genes are shown in Supplemental Figure 2 online and Table 3. The cutoff value was set according to Aoki et al (2007). The clusters of coexpressed flavonoid genes were classified into two major groups.…”