基于Cytoscape的蛋白质网络可视化聚类分析插件

蛋白质网络聚类是识别功能模块的重要手段,不仅有利于理解生物系统的组织结构,对预测蛋白质功能也具有重要的意义.聚类结果的可视化分析是实现蛋白质网络聚类的有效途径.本论文基于开源的Cytoscape平台,设计并实现了一个蛋白质网络聚类分析及可视化插件CytoCluster.该插件集成了MCODE,FAG-EC,HC-PIN,OH-PIN,IPCA,EAGLE等六种典型的聚类算法;实现了聚类结果的可视化,将分析所得的clusters以缩略图列表的形式直观地显示出来,对于单个cluster,可显示在原网络中的位置,并能生成相应的子图单独显示;可对聚类结果进行导出,记录了算法名称、参数、聚类结果等信息.该插件具有良好的扩展性,提供了统一的算法接口,可不断添加新的聚类算法.

A Cytoscape plugin for visualization and clustering analysis of protein interaction networks

Clustering analysis is an important way to identify potential functional modules in protein interaction networks. It not only helps to understand the constitutional structure of biological systems, but also is of great significance to predict protein function. Visualization of clustering results is an effective way to realize protein network clustering. Based on the open-source platform Cytoscape, a plugin called CytoCluster for clustering analysis and visualization of protein interaction network has been designed and achieved. This plugin implements six typical clustering algorithms called MCODE, FAG-EC, HC-PIN, OH-PIN, IPCA, EAGLE, provides the visualization of clustering results, where clusters are intuitively presented in the form of a thumbnail list. For a single cluster, CytoCluster can display its location in the original network and generate the new sub-network to show the selected cluster separately. It can export results to text file, recording the name of algorithms, parameters, and the clustering results. CytoCluster has a good scalability, providing unified algorithm interface. New clustering algorithms could be constantly extended into it.