Approaches for extracting practical information from gene co-expression networks in plant biology.
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.
Aoki
Koh
K
Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, 292-0818, Japan.
Ogata
Yoshiyuki
Y
Shibata
Daisuke
D
D017360:Arabidopsis / Q000235:genetics; D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis; D010944:Plants / Q000235:genetics* / Q000378:metabolism; D049490:Systems Biology; D013729:Terpenes / Q000378:metabolism
D013729:Terpenes