Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network  

作　　者：Pengcheng Zhu Haibin Gu Yinming Jiao Donglin Huang Ming Chen 

机构地区：[1]Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China [2]James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China [3]State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China

出　　处：《Genomics, Proteomics & Bioinformatics》2011年第4期128-137,共10页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant No.30771326,30971743,31050110121);the National Science and Technology Project of China(Grant No.2008AA10Z125,2008ZX08003-005,2009DFA32030);the Program for New Century Excellent Talents in University of China(Grant No.NCET-07-0740)

摘　　要：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：//bis.zju.edu.cn/ 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.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：//bis.zju.edu.cn/ 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 

分 类 号：Q811.4[生物学—生物工程] TS210.1[轻工技术与工程—粮食、油脂及植物蛋白工程]