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| PNmerger: 一个整合生物学通路和蛋白质相互作用网络的Cytoscape插件 | |
| 引用本文： | 孙汉昌,李栋,王建,刘中扬,朱云平,谢红卫,贺福初. PNmerger: 一个整合生物学通路和蛋白质相互作用网络的Cytoscape插件[J]. 生物化学与生物物理进展, 2009, 36(12): 1613-1616. DOI: 10.3724/SP.J.1206.2009.00236 |
| 作者姓名： | 孙汉昌 李栋 王建 刘中扬 朱云平 谢红卫 贺福初 |
| 作者单位： | 1. 国防科技大学机电工程与自动化学院自动控制系,长沙,410073;蛋白质组学国家重点实验室,北京蛋白质组研究中心,军事医学科学院放射与辐射医学研究所,北京,102206 2. 蛋白质组学国家重点实验室,北京蛋白质组研究中心,军事医学科学院放射与辐射医学研究所,北京,102206 3. 国防科技大学机电工程与自动化学院自动控制系,长沙,410073 |
| 基金项目： | 国家重点基础研究发展计划(973)资助项目(2006CB910803, 2006CB910706), 国家高技术研究发展计划(863)资助项目(2006AA02A312), 国家科技重大专项( 2008ZX10002-016, 2009ZX09301-002), 国家自然科学基金(30621063, 30800200)和蛋白质组学国家重点实验室课题(SKLP-Y200811)资助项目. |
| 摘 要： | Cytoscape是一个广泛应用于分子相互作用网络可视化的软件．发展了一个基于java的Cytoscape插件PNmerger．对于一个蛋白质相互作用网络，PNmerger能够使用KEGG数据库中的通路信息自动注释网络中的蛋白质．并通过网络和通路的比较发现网络中已知的通路元件，预测可能的通路元件及通路交联元件．该软件可以可视化网络中存在的通路模块，并将连接不同通路间的潜在交联元件显示出来．PNmerger软件能够有效地帮助实验人员发现网络中重要的功能线索，帮助实验人员进行实验设计．用户可以通过网站http://www.hupo.org.cn/PNmerger下载PNmerger插件． |
| 关 键 词： | 系统生物学，生物学通路，蛋白质-蛋白质相互作用，交联元件，通路扩展，cytoscape插件 |
| 收稿时间： | 2009-04-14 |
| 修稿时间： | 2009-05-05 |
PNmerger: a Cytoscape Plugin to Merge Biological Pathways and Protein Interaction Networks |
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| SUN Han-Chang,LI Dong,WANG Jian,LIU Zhong-Yang,Zhu Yun-Ping,XIE Hong-Wei and HE Fu-Chu. PNmerger: a Cytoscape Plugin to Merge Biological Pathways and Protein Interaction Networks[J]. Progress In Biochemistry and Biophysics, 2009, 36(12): 1613-1616. DOI: 10.3724/SP.J.1206.2009.00236 | |
| Authors: | SUN Han-Chang LI Dong WANG Jian LIU Zhong-Yang Zhu Yun-Ping XIE Hong-Wei HE Fu-Chu |
| Affiliation: | Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha 410073, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China;Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha 410073, China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China |
| Abstract: | PNmerger (a biological Pathway and protein Network merger) is a java based plugin for the widely used open source Cytoscape molecular interaction viewer. For a protein interaction network, PNmerger can automatically annotate the network proteins with the KEGG pathway information, find the known pathway elements in protein network, and predict the possible pathway elements. To present the pathway information for the protein network, PNmerger illustrates the clusters of the nodes with the same biological pathway, and also presents the potential crosstalk elements between different pathways. This information will be helpful for the users to find the important clues for knowledge discovery and experimental design. PNmerger is available online at http://www.hupo.org.cn/PNmerger. |
| Keywords: | systems biology biological pathway protein-protein interactions crosstalk elements pathway expanding cytoscape plugin |
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