clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
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clusterMaker：Cytoscape 的多算法聚类插件。
DOI：
10.1186/1471-2105-12-436
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发表时间：
2011-11-09
影响因子：
3
通讯作者：
Ferrin TE
中科院分区：
文献类型：
--
作者：
Morris JH;Apeltsin L;Newman AM;Baumbach J;Wittkop T;Su G;Bader GD;Ferrin TE
在后基因组时代，高通量数据的快速增长需要能够整合不同类型数据并促进识别其中具有生物学意义的模式的计算工具。例如，蛋白质-蛋白质相互作用数据集已被聚类以识别稳定的复合物，但科学家缺乏易于访问的工具来促进来自不同类型实验的多个数据集的组合分析。在这里，我们提出了clusterMaker，Cytoscape插件，实现了几个聚类算法，并提供网络，树状图和热图的结果视图。Cytoscape网络与所有其他视图相链接，因此其中一个视图中的选择会立即反映在其他视图中。clusterMaker是第一个Cytoscape插件，实现了各种各样的聚类算法和可视化，包括分层聚类，树状图加热图可视化（树视图），k-means，k-medoid，SCPS，AutoSOME和原生（Java）MCL的唯一实现。结果以三种用途：使用最近发表的小鼠相互作用组和近100种不同细胞/组织类型的小鼠微阵列数据集分析蛋白质表达数据;鉴定酵母酿酒酵母中的蛋白质复合物;以及邻位氧螯合物（VOC）酶超家族的聚类分析。对于场景一，我们探索功能丰富的小鼠interactomes特定的细胞表型，并应用模糊聚类。对于第二种情况，我们探索的prefoldin复杂的详细使用物理和遗传相互作用集群。对于第三种情况，我们探索了VOC超家族中甲基丙二酰辅酶A差向异构酶蛋白质的可能注释。所有这三种方案的Cytoscape会话文件都在Additional Files部分提供。Cytoscape插件clusterMaker提供了许多聚类算法和可视化，可单独或组合用于生物数据集的分析和可视化，以及确认或生成有关生物功能的假设。其中一些可视化和算法仅可通过clusterMaker插件提供给Cytoscape用户。clusterMaker可通过Cytoscape插件管理器获得。
In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL. Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section. The Cytoscape plugin clusterMaker provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the clusterMaker plugin. clusterMaker is available via the Cytoscape plugin manager.
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影响因子：
14.9
作者：
Krause, A;Haas, SA;Vingron, M
通讯作者：
Vingron, M
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作者：
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通讯作者：
Superti-Furga, G
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作者：
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通讯作者：
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