Network-Based Approaches for Pathway Level Analysis.
Network-Based Approaches for Pathway Level Analysis.
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DOI：
10.1002/cpbi.42
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发表时间：
2018-03-01
影响因子：
--
通讯作者：
Draghici, Sorin
中科院分区：
文献类型：
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作者：
Nguyen, Tin;Mitrea, Cristina;Draghici, Sorin
识别受影响的途径是一个重要问题，因为它使我们能够在检测差异表达基因之外深入了解基础生物学。在过去的十年中，已经为此目的开发了大量的方法。上一代的通路分析方法被设计为考虑通路拓扑结构的各个方面，以提高结果的准确性。在这里，我们涵盖了34个这样的拓扑结构为基础的途径分析方法在过去的13年中发表。我们比较了这些方法与实施、可用性、输入格式、图模型以及用于计算途径水平统计数据和统计显著性的统计方法相关的类别。我们还讨论了一些关键的挑战，需要解决的问题，出现在方法和途径的代表性，包括不一致的术语，数据格式，缺乏有意义的基准，更重要的是，一个系统的偏见，是目前在大多数现有的方法。John Wiley & Sons，Inc.
Identification of impacted pathways is an important problem because it allows us to gain insights into the underlying biology beyond the detection of differentially expressed genes. In the past decade, a plethora of methods have been developed for this purpose. The last generation of pathway analysis methods are designed to take into account various aspects of pathway topology in order to increase the accuracy of the findings. Here, we cover 34 such topology-based pathway analysis methods published in the past 13 years. We compare these methods on categories related to implementation, availability, input format, graph models, and statistical approaches used to compute pathway level statistics and statistical significance. We also discuss a number of critical challenges that need to be addressed, arising both in methodology and pathway representation, including inconsistent terminology, data format, lack of meaningful benchmarks, and, more importantly, a systematic bias that is present in most existing methods. © 2018 by John Wiley & Sons, Inc.