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Computational Identification of Protein-Protein Interactions in rice Based on the Predicted rice interactome Network

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Genomics, Proteomics & Bioinformatics 2011年第4期9卷 128-137页

作者： Pengcheng Zhu Haibin Gu Yinming Jiao Donglin Huang Ming Chen Department of Bioinformatics College of Life Sciences Zhejiang University Hangzhou 310058 China James D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310058 China State Key Laboratory of Plant Physiology and Biochemistry College of Life Sciences Zhejiang University Hangzhou 310058 China

Plant protein-protein interaction networks have not been identified by large-scale experiments. In order to better understand the protein interactions in rice, the Predicted rice interactome Network （PRIN; http：//***/ prin/） presented 76,585 predicted interactions involving 5,049 rice proteins. After mapping genomic features of rice （GO annotation, subcellular localizationprediction, and gene expression）, we found that a well-annotated and biologically significant network is rich enough to capture many significant functional linkages within higher-order biological systems, such as pathways and biological processes. Furthermore, we took MADS-box do- main-containing proteins and circadian rhythm signaling pathways as examples to demonstrate that functional protein complexes and biological pathways could be effectively expanded in our predicted network. The expanded molecular network in PRIN has considerably improved the capability of these analyses to integrate existing knowledge and provide novel insights into the function and coordination of genes and gene networks.

关键词： protein-protein interactions rice interactome interolog sub-network expansion pathway clustering

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Computational Identification of Protein-Protein Interactions in rice Based on the Predicted rice interactome Network

引用

Genomics,Proteomics & Bioinformatics 2011年第Z2期 128-137页

作者： Pengcheng Zhu1, Haibin Gu1, Yinming Jiao1, Donglin Huang1,2, and Ming Chen1,2,3 1Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China 2James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China 3State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China

Plant protein-protein interaction networks have not been identified by large-scale experiments. In order to better understand the protein interactions in rice, the Predicted rice interactome Network (PRIN; http://***/ prin/) presented 76,585 predicted interactions involving 5,049 rice proteins. After mapping genomic features of rice (GO annotation, subcellular localization prediction, and gene expression), we found that a well-annotated and biologically significant network is rich enough to capture many significant functional linkages within higher-order biological systems, such as pathways and biological processes. Furthermore, we took MADS-box do- main-containing proteins and circadian rhythm signaling pathways as examples to demonstrate that functional protein complexes and biological pathways could be effectively expanded in our predicted network. The expanded molecular network in PRIN has considerably improved the capability of these analyses to integrate existing knowledge and provide novel insights into the function and coordination of genes and gene networks.

关键词： protein-protein interactions rice interactome interolog sub-network expansion pathway clustering

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