Using biological networks to integrate, visualize and analyze genomics data.
Using biological networks to integrate, visualize and analyze genomics data.
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DOI：
10.1186/s12711-016-0205-1
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发表时间：
2016-03-31
期刊：
影响因子：
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通讯作者：
Lynn DJ
中科院分区：
文献类型：
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作者：
Charitou T;Bryan K;Lynn DJ
网络生物学是生物医学研究的一个快速发展的领域，反映了当前的观点，即复杂的表型，如疾病易感性，不是孤立作用的单个基因突变的结果，而是由于基因的网络环境的扰动。了解这些分子相互作用网络的拓扑结构，并确定在其结构和调控中发挥核心作用的分子是理解复杂系统的关键。下一代测序成本的下降现在使研究人员能够在全基因组范围内以及在大量不同条件下对这些网络的分子组成进行常规编目。在这篇综述中，我们描述了如何使用公开可用的生物信息学工具，将全基因组的“组学”数据整合到实验支持的分子相互作用网络中。此外，我们描述了如何可视化和分析这些网络，以确定可能的功能相关的拓扑特征，包括网络枢纽，瓶颈和模块。我们表明，网络生物学提供了一个强大的概念方法来整合和发现全基因组基因组数据的模式，但我们也讨论了这些方法的局限性和警告，采用这些方法的研究人员必须保持意识。本文的在线版本（doi：10.1186/s12711-016-0205-1）包含补充材料，可供授权用户使用。
Network biology is a rapidly developing area of biomedical research and reflects the current view that complex phenotypes, such as disease susceptibility, are not the result of single gene mutations that act in isolation but are rather due to the perturbation of a gene’s network context. Understanding the topology of these molecular interaction networks and identifying the molecules that play central roles in their structure and regulation is a key to understanding complex systems. The falling cost of next-generation sequencing is now enabling researchers to routinely catalogue the molecular components of these networks at a genome-wide scale and over a large number of different conditions. In this review, we describe how to use publicly available bioinformatics tools to integrate genome-wide ‘omics’ data into a network of experimentally-supported molecular interactions. In addition, we describe how to visualize and analyze these networks to identify topological features of likely functional relevance, including network hubs, bottlenecks and modules. We show that network biology provides a powerful conceptual approach to integrate and find patterns in genome-wide genomic data but we also discuss the limitations and caveats of these methods, of which researchers adopting these methods must remain aware. The online version of this article (doi:10.1186/s12711-016-0205-1) contains supplementary material, which is available to authorized users.