Co-expression network analysis is one of the most powerful approaches for interpretation of large transcriptomic datasets.It enables characterization of modules of co-expressed genes that may share biological functional linkages.Such networks provide an initial way to explore functional associations from gene expression profiling and can be applied to various aspects of plant biology.This review presents the applications of co-expression network analysis in plant biology and addresses optimized strategies from the recent literature for performing co-expression analysis on plant biological systems.Additionally,we describe the combined interpretation of co-expression analysis with other genomic data to enhance the generation of biologically relevant information.