Adamcsek Balázs, Palla Gergely, Farkas Illés J, Derényi Imre, Vicsek Tamás
Department of Biological Physics, Eötvös University, Pázmány P. stny. 1A, H-1117 Budapest, Hungary.
Bioinformatics. 2006 Apr 15;22(8):1021-3. doi: 10.1093/bioinformatics/btl039. Epub 2006 Feb 10.
Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein association network modules appear as groups of densely interconnected nodes, also called communities or clusters. These modules often overlap with each other and form a network of their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of these groups. We show that in gene (protein) association networks CFinder can be used to predict the function(s) of a single protein and to discover novel modules. CFinder is also very efficient for locating the cliques of large sparse graphs.
CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering.
Supplementary data are available on Bioinformatics online.
大多数细胞任务并非由单个蛋白质执行,而是由功能相关的蛋白质组来完成,这些蛋白质组通常被称为模块。在蛋白质关联网络中,模块表现为紧密相连的节点组,也称为群落或簇。这些模块常常相互重叠,形成一个自身的网络,其中节点(链接)代表模块(重叠部分)。我们引入了CFinder,这是一个快速程序,用于在无向图中定位和可视化重叠的、紧密相连的节点组,并允许用户在原始图和这些组的网络之间轻松导航。我们表明,在基因(蛋白质)关联网络中,CFinder可用于预测单个蛋白质的功能并发现新的模块。CFinder在定位大型稀疏图的团方面也非常高效。
CFinder(适用于Windows、Linux和Macintosh)及其手册可从http://angel.elte.hu/clustering下载。
补充数据可在《生物信息学》在线获取。