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An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice

Liu, Lili ; Mei, Qian ; Yu, Zhenning ; Sun, Tianhao ; Zhang, Zijun ; Chen, Ming

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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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’ 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.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Liu, Lili ; Mei, Qian ; Yu, Zhenning ; Sun, Tianhao ; Zhang, Zijun ; Chen, Ming  (2013)  An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 10(2), 2013

Online-Journal: http://journal.imbio.de/article.php?aid=223
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2013/5269



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