-------- Original Message -------- Subject: Mini Review: Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology Date: Tue, 29 May 2007 09:16:01 +0200 From: Klaas Vandepoele <Klaas.Vandepoele@psb.ugent.be> To: Tineke Casneuf <ticas@psb.ugent.be>, Steven Maere <stmae@psb.ugent.be> CC: Yves Van de Peer <yvdp@psb.ugent.be> Mini Review 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 geneprioritization, and provides novel insights into the system-level understanding of plant cellular processes. Aoki et al. (2007)PlantCellPhysiol48,381.pdf -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, UGent Technologiepark 927, B-9052 Gent, Belgium E-mail: Klaas.Vandepoele@psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ================================================================== -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer@psb.ugent.be http://www.psb.ugent.be/bioinformatics/