MarVis: a tool for clustering and visualization of metabolic biomarkers.
MarVis: a tool for clustering and visualization of metabolic biomarkers.
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DOI：
10.1186/1471-2105-10-92
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发表时间：
2009-03-20
影响因子：
3
通讯作者：
Meinicke P
中科院分区：
文献类型：
--
作者：
Kaever A;Lingner T;Feussner K;Göbel C;Feussner I;Meinicke P
系统生物学实验研究的一个中心目标是识别隐藏在源自代谢组学实验的大规模分析强度测量数据的扩散背景中的有意义的标记。基于强度的聚类是一种基于相似强度分布的分组来识别代谢标志物的无监督方法。这种基本方法的一个主要问题是，在一般情况下，没有足够数量的生物相关的集群的先验信息。我们提出的工具MarVis（标记可视化）的强度为基础的配置文件使用一维自组织映射（1D-SOM）的数据挖掘。MarVis可以导入和导出可自定义的CSV（逗号分隔值）文件，并提供聚合和归一化例程，用于预处理包含许多不同实验条件下重复测量的强度曲线。然后通过训练1D-SOM模型来实现鲁棒聚类，该模型引入了基于相似性的强度分布排序。排序允许数据内的强度变化的方便可视化，并且促进聚类到更大块中的交互式聚合。基于强度的可视化与附加数据属性的呈现相结合，可以进一步支持实验数据的分析。MarVis是一个用户友好的交互式工具，用于探索大量实验强度分布中的复杂图案变化。1D-SOM的应用提供了一个方便的概述相关的配置文件和配置文件组。专门的可视化有效地支持研究人员分析大量的推定集群，即使生物学上有意义的群体的真实数量是未知的。虽然MarVis已开发用于代谢组学数据的分析，但该工具也可应用于基因表达数据。
A central goal of experimental studies in systems biology is to identify meaningful markers that are hidden within a diffuse background of data originating from large-scale analytical intensity measurements as obtained from metabolomic experiments. Intensity-based clustering is an unsupervised approach to the identification of metabolic markers based on the grouping of similar intensity profiles. A major problem of this basic approach is that in general there is no prior information about an adequate number of biologically relevant clusters. We present the tool MarVis (Marker Visualization) for data mining on intensity-based profiles using one-dimensional self-organizing maps (1D-SOMs). MarVis can import and export customizable CSV (Comma Separated Values) files and provides aggregation and normalization routines for preprocessing of intensity profiles that contain repeated measurements for a number of different experimental conditions. Robust clustering is then achieved by training of an 1D-SOM model, which introduces a similarity-based ordering of the intensity profiles. The ordering allows a convenient visualization of the intensity variations within the data and facilitates an interactive aggregation of clusters into larger blocks. The intensity-based visualization is combined with the presentation of additional data attributes, which can further support the analysis of experimental data. MarVis is a user-friendly and interactive tool for exploration of complex pattern variation in a large set of experimental intensity profiles. The application of 1D-SOMs gives a convenient overview on relevant profiles and groups of profiles. The specialized visualization effectively supports researchers in analyzing a large number of putative clusters, even though the true number of biologically meaningful groups is unknown. Although MarVis has been developed for the analysis of metabolomic data, the tool may be applied to gene expression data as well.
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影响因子：
5.8
作者：
Eichler, GS;Huang, S;Ingber, DE
通讯作者：
Ingber, DE
影响因子：
4.8
作者：
Glauser, Gaetan;Grata, Elia;Wolfender, Jean-Luc
通讯作者：
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影响因子：
46.9
作者：
Fiehn, O;Kopka, J;Willmitzer, L
通讯作者：
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影响因子：
7.4
作者：
Malitsky, Sergey;Blum, Eyal;Aharoni, Asaph
通讯作者：
Aharoni, Asaph
DOI：
10.1073/pnas.96.6.2907
发表时间：
1999-03-16
影响因子：
11.1
作者：
Tamayo, P;Slonim, D;Golub, TR
通讯作者：
Golub, TR