An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice
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 de...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2013-06-01
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| Series: | Journal of Integrative Bioinformatics |
| Online Access: | https://doi.org/10.1515/jib-2013-223 |
| _version_ | 1818587344644603904 |
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| author | Liu Lili Mei Qian Yu Zhenning Sun Tianhao Zhang Zijun Chen Ming |
| author_facet | Liu Lili Mei Qian Yu Zhenning Sun Tianhao Zhang Zijun Chen Ming |
| author_sort | Liu Lili |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-16T09:07:22Z |
| format | Article |
| id | doaj.art-1088caeb74444ca797cadb78f3c1b572 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-16T09:07:22Z |
| publishDate | 2013-06-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-1088caeb74444ca797cadb78f3c1b5722022-12-21T22:37:03ZengDe GruyterJournal of Integrative Bioinformatics1613-45162013-06-011029410210.1515/jib-2013-223biecoll-jib-2013-223An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of RiceLiu Lili0Mei Qian1Yu Zhenning2Sun Tianhao3Zhang Zijun4Chen Ming5College of Life Sciences, Zhejiang University, Hangzhou, 310058, ChinaCollege of Life Sciences, Zhejiang University, Hangzhou, 310058, ChinaCollege of Life Sciences, Zhejiang University, Hangzhou, 310058, ChinaCollege of Life Sciences, Zhejiang University, Hangzhou, 310058, ChinaCollege of Life Sciences, Zhejiang University, Hangzhou, 310058, ChinaCollege of Life Sciences, Zhejiang University, Hangzhou, 310058, ChinaUnderstanding 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.https://doi.org/10.1515/jib-2013-223 |
| spellingShingle | Liu Lili Mei Qian Yu Zhenning Sun Tianhao Zhang Zijun Chen Ming An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice Journal of Integrative Bioinformatics |
| title | An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice |
| title_full | An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice |
| title_fullStr | An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice |
| title_full_unstemmed | An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice |
| title_short | An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice |
| title_sort | integrative bioinformatics framework for genome scale multiple level network reconstruction of rice |
| url | https://doi.org/10.1515/jib-2013-223 |
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