title: An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice.
abstract: Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology. Genome-wide association studies (GWAS) statistically connect genotypes to phenotypes, without any recourse to known molecular interactions, whereas a molecular mechanistic description ties gene function to phenotype through gene regulatory networks (GRNs), protein-protein interactions (PPIs) and molecular pathways. Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes. However, the lack of curated metabolic model of rice is blocking the exploration of genome-scale multi-level network reconstruction. Here, we have merged GRNs, PPIs and genome-scale metabolic networks (GSMNs) approaches into a single framework for rice via omics&rsquo; regulatory information reconstruction and integration. Firstly, we reconstructed a genome-scale metabolic model, containing 4,462 function genes, 2,986 metabolites involved in 3,316 reactions, and compartmentalized into ten subcellular locations. Furthermore, 90,358 pairs of protein-protein interactions, 662,936 pairs of gene regulations and 1,763 microRNA-target interactions were integrated into the metabolic model. Eventually, a database was developped for systematically storing and retrieving the genome-scale multi-level network of rice. This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.
authors.affiliation: College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Liu
authors.forename: Qian
authors.initials: Q
authors.lastname: Mei
authors.forename: Zhenning
authors.initials: Z
authors.lastname: Yu
authors.forename: Tianhao
authors.initials: T
authors.lastname: Sun
authors.forename: Zijun
authors.initials: Z
authors.lastname: Zhang
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D020407:Internet; D012275:Oryza / Q000235:genetics*