Pan- and core- network analysis of co-expression genes in a model plant

Abstract

Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of pan-network and core-network representing union and intersection between a sizeable fractions of individual networks, respectively. We showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.\n\nResearch AreaSystems and Synthetic Biology\n\nSummaryBy analyzing 134 microarray datasets for Arabidopsis, we found that gene coexpression networks are highly context-dependent.\n\nFinancial sourceWork at Brookhaven was supported by grants PM-031 from the Office of Biological Research of the U.S. Department of Energy.