Comparative microbial modules resource: generation and visualization of multi-species biclusters.
Comparative microbial modules resource: generation and visualization of multi-species biclusters.
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DOI：
10.1371/journal.pcbi.1002228
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发表时间：
2011-12
影响因子：
4.3
通讯作者：
Bonneau R
中科院分区：
文献类型：
--
作者：
Kacmarczyk T;Waltman P;Bate A;Eichenberger P;Bonneau R
许多密切相关的生物体的大规模、高通量数据集的日益丰富，为通过同时对多个物种的数据集进行双聚类进行比较分析提供了机会。这些分析需要重新制定如何组织多物种数据集和可视化比较基因组数据分析结果。最近，我们开发了一种方法，多物种cMonkey，它集成了来自多个物种的异构高通量数据类型来识别保守的调控模块。在这里，我们提出了一个基于 Gaggle 构建的集成数据可视化系统，可以探索我们方法的结果（可在 http://meatwad.bio.nyu.edu/cmmr.html 获取）。该系统还可用于探索其他比较基因组学数据集和其他数据分析程序的输出——其他多物种聚类程序或不同单物种数据集的独立聚类的结果。我们提供了将我们的系统用于两种细菌（大肠杆菌和鼠伤寒沙门氏菌）的示例。我们通过探索参与氮代谢的保守双簇来说明我们的系统的用途，揭示了 yjjI 的假定功能，yjjI 是一个目前尚未表征的基因，我们预测它参与氮同化。先进的高通量实验技术正在为多个相关物种在多个信息水平（例如 mRNA、蛋白质、相互作用、功能测定等）提供全基因组测量。我们提出了一种双聚类算法和相关的可视化系统，用于生成和探索从综合多物种基因组数据集分析中得出的调控模块。我们使用多物种 cMonkey，这是我们自己构建的一种算法，可以整合来自多个物种的不同系统生物学数据类型，形成双簇或条件依赖性调节模块，这些模块在分析的多个物种和特定于处理物种子集的双簇中都是保守的。我们的资源是一个基于 Web 和 Java 的集成系统，允许生物学家在数据、两个物种的关联网络以及两个物种的现有注释的背景下探索保守的和物种特异性的双簇。我们这项工作的重点是使用集成系统，并从探索与两种革兰氏阴性细菌（大肠杆菌和鼠伤寒沙门氏菌）氮代谢相关的模块中提取示例。
The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures – results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation. Advancing high-throughput experimental technologies are providing access to genome-wide measurements for multiple related species on multiple information levels (e.g. mRNA, protein, interactions, functional assays, etc.). We present a biclustering algorithm and an associated visualization system for generating and exploring regulatory modules derived from analysis of integrated multi-species genomics datasets. We use multi-species-cMonkey, an algorithm of our own construction that can integrate diverse systems-biology datatypes from multiple species to form biclusters, or condition-dependent regulatory modules, that are conserved across both the multiple species analyzed and biclusters that are specific to subsets of the processed species. Our resource is an integrated web and java based system that allows biologists to explore both conserved and species-specific biclusters in the context of the data, associated networks for both species, and existing annotations for both species. Our focus in this work is on the use of the integrated system with examples drawn from exploring modules associated with nitrogen metabolism in two Gram-negative bacteria, E. coli and S. Typhimurium.
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影响因子：
14.9
作者：
Faith JJ;Driscoll ME;Fusaro VA;Cosgrove EJ;Hayete B;Juhn FS;Schneider SJ;Gardner TS
通讯作者：
Gardner TS
影响因子：
64.5
作者：
Bonneau, Richard;Facciotti, Marc T.;Baliga, Nitin S.
通讯作者：
Baliga, Nitin S.
影响因子：
3
作者：
Baitaluk, M;Qian, XF;Gupta, A
通讯作者：
Gupta, A
影响因子：
7
作者：
Alm, EJ;Huang, KH;Arkin, AP
通讯作者：
Arkin, AP
影响因子：
1.7
作者：
Ben-Dor, A;Chor, B;Yakhini, Z
通讯作者：
Yakhini, Z