Buck Institute for Age Research, Novato, California, USA.
Nat Protoc. 2011 Mar;6(3):285-95. doi: 10.1038/nprot.2010.197. Epub 2011 Feb 10.
Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.
连通聚类是一种将生物数据分割成相似对象组的方法，例如基因。它提供了对各种功能的集成访问，这些功能解决了典型聚类分析的每一步。为了便于使用，连通聚类在线提供了三个用户友好的界面：功能强大的独立版本、网络界面和 Cytoscape 插件集。在本文中，我们描述了三个主要工作流程：（i）使用 Cytoscape 进行蛋白质（超）家族检测，（ii）使用不完整的金标准进行蛋白质同源性检测，以及（iii）基因表达数据聚类。本方案指导用户了解连通聚类的最重要功能，大约需要 1 小时完成。
