A CLUSTERING ENVIRONMENT FOR CYTOSCAPE

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 目标是为Cytoscape环境提供集群插件的组合。给定一个任意加权的无向相似图（SG）。该图可以例如（i）通过使用SFLDLoader（其查询结构功能链接数据库）或（ii）通过使用all-vs.-所有BLAST结果文件。随后，可以使用特殊的插件（i）使用层次聚类（HC）、马尔可夫聚类（MCL）、加权图聚类编辑（WGCE）和连接组件分析来对图进行聚类，或者（ii）探索关于几个特定于上下文的问题的这些聚类。给定一个簇内的蛋白质，人们可能会对簇的列表感兴趣，按蛋白质与簇的相似性排序。另一个例子是对给定聚类中的所有蛋白质进行评分，以了解它们与所有其他元素的相似性（中心性分析）。InterpreterExplorer的一个主要目标是协助SFLD数据的手动后注释。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The goal is to provide a combination of clustering plug-ins for the Cytoscape environment. Given an arbitrary weighted, undirected similarity graph (SG). This graph can be created for instance (i) by using the SFLDLoader, which queries the Structure Function Linkage Database, or (ii) by using all-vs.-all BLAST result files. Subsequently, special plug-ins may be used (i) to cluster the graph with Hierarchical Clustering (HC), Markov Clustering (MCL), Weighted Graph Cluster Editing (WGCE), and Connected Component analysis or (ii) to explore these clusters regarding several context-specific questions. Given a protein within a cluster, one might be interested in a list of clusters, ordered by protein-to-cluster similarities. Another example would be a scoring of all proteins within a given cluster regarding their similarity to all other elements (centrality analysis). One major goal of the ClusterExplorer is to assist with the manual post-annotation of SFLD data.