J Integr Bioinform - An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice.

Tópicos

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Resumo

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’ 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.

Resumo Limpo

understand metabol reaction translat genom organ phenotyp grand challeng biolog genomewid associ studi gwas statist connect genotyp phenotyp without recours known molecular interact wherea molecular mechanist descript tie gene function phenotyp gene regulatori network grns proteinprotein interact ppis molecular pathway integr differ regulatori inform level organ expect provid good way map genotyp phenotyp howev lack curat metabol model rice block explor genomescal multilevel network reconstruct merg grns ppis genomescal metabol network gsmns approach singl framework rice via omicsrsquo regulatori inform reconstruct integr first reconstruct genomescal metabol model contain function gene metabolit involv reaction compartment ten subcellular locat furthermor pair proteinprotein interact pair gene regul micrornatarget interact integr metabol model eventu databas develop systemat store retriev genomescal multilevel network rice provid refer understand genotypephenotyp relationship rice analysi molecular regulatori network

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