From sequencing data to gene functions: co-functional network approaches
From sequencing data to gene functions: co-functional network approaches
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DOI：
10.1080/19768354.2017.1284156
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发表时间：
2017-02-01
影响因子：
2.9
通讯作者：
Lee, Insuk
中科院分区：
文献类型：
--
作者：
Shim, Jung Eun;Lee, Tak;Lee, Insuk
先进的高通量测序技术在公共数据库中积累了大量的基因组学和转录组学数据。由于技术的高度可及性，DNA和RNA测序在包括动物和农作物在内的大多数物种的基因功能研究中具有巨大潜力。一种将测序数据转化为基因功能信息的成熟分析平台是共功能网络。因为所有基因都是通过与其他基因的相互作用来发挥其功能的，所以网络分析是研究基因功能的一种合理方法。基于网络的功能研究工作流程由三个步骤组成：（i）推断共功能链接，（ii）评估这些链接并将其整合到基因组规模的网络中，（iii）从网络中生成功能假设。共功能链接可以通过系统发育谱分析、基因邻域分析、结构域谱分析、关联分析以及来自RNA测序数据的共表达分析从DNA测序数据中推断出来。然后，在金标准共功能链接的帮助下，对推断出的链接进行评估并整合到基因组规模的网络中。可以基于（i）网络连通性，（ii）网络传播，（iii）子网络分析从网络中生成功能假设。这里描述的功能分析流程只需要测序数据，而下一代测序技术可以很容易地为大多数物种提供这些数据。因此，共功能网络将极大地促进测序数据在任何细胞生物的遗传学研究中的应用。
Advanced high-throughput sequencing technology accumulated massive amount of genomics and transcriptomics data in the public databases. Due to the high technical accessibility, DNA and RNA sequencing have huge potential for the study of gene functions in most species including animals and crops. A proven analytic platform to convert sequencing data to gene functional information is co-functional network. Because all genes exert their functions through interactions with others, network analysis is a legitimate way to study gene functions. The workflow of network-based functional study is composed of three steps: (i) inferencing co-functional links, (ii) evaluating and integrating the links into genome-scale networks, and (iii) generating functional hypotheses from the networks. Co-functional links can be inferred from DNA sequencing data by using phylogenetic profiling, gene neighborhood, domain profiling, associalogs, and co-expression analysis from RNA sequencing data. The inferred links are then evaluated and integrated into a genome-scale network with aid from gold-standard co-functional links. Functional hypotheses can be generated from the network based on (i) network connectivity, (ii) network propagation, and (iii) subnetwork analysis. The functional analysis pipeline described here requires only sequencing data which can be readily available for most species by next-generation sequencing technology. Therefore, co-functional networks will greatly potentiate the use of the sequencing data for the study of genetics in any cellular organism.