Comparison of multiple metagenomes using phylogenetic networks based on ecological indices
Comparison of multiple metagenomes using phylogenetic networks based on ecological indices
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DOI：
10.1038/ismej.2010.51
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发表时间：
2010-10-01
期刊：
影响因子：
11
通讯作者：
Huson, Daniel H.
中科院分区：
文献类型：
--
作者：
Mitra, Suparna;Gilbert, Jack A.;Huson, Daniel H.
第二代测序技术正在推动超基因组项目的数量和范围的大幅增加。非常需要开发新的方法来可视化多个元基因组数据集之间的关系。为了解决这一问题，提出了一种新的方法，该方法结合使用分类分析、生态指数和非层次聚类来提供不同元基因组数据集之间关系的网络表示。使用几个不同类型的已发表数据集说明了这一方法，包括元基因组、元翻译和16S核糖体图谱。将该方法应用于在不同分类水平上总结的相同数据，产生了非常相似的网络，表明该分析非常稳健。重要的是，网络为样本之间的非根深蒂固的关系提供了可视的定义和度量量化，将其他工具的期望特征结合在一起。《ISME期刊》(2010年)第4期，第1236-1242号；doi：10.1038/ismej.2010.51；2010年4月29日在线出版
Second-generation sequencing technologies are fueling a vast increase in the number and scope of metagenome projects. There is a great need for the development of new methods for visualizing the relationships between multiple metagenomic data sets. To address this, a novel approach is presented that combines the use of taxonomic analysis, ecological indices and non-hierarchical clustering to provide a network representation of the relationships between different metagenome data sets. The approach is illustrated using several published data sets of different types, including metagenomes, metatranscriptomes and 16S ribosomal profiles. Application of the approach to the same data summarized at different taxonomical levels gives rise to remarkably similar networks, indicating that the analysis is very robust. Importantly, the networks provide the both visual definition and metric quantification for the non-rooted relationship between samples, combining the desirable characteristics of other tools into one. The ISME Journal (2010) 4, 1236-1242; doi:10.1038/ismej.2010.51; published online 29 April 2010