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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Identification of Gene Networks with Time Delayed Regulation Based on Temporal Expression Profiles
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Identification of Gene Networks with Time Delayed Regulation Based on Temporal Expression Profiles

机译：基于时间表达谱的时滞调控基因网络识别

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摘要

There are fundamental limitations in inferring the functional interaction structure of a gene (regulatory) network only from sequence information such as binding motifs. To overcome such limitations, various approaches have been developed to infer the functional interaction structure from expression profiles. However, most of them have not been so successful due to the experimental limitations and computational complexity. Hence, there is a pressing need to develop a simple but effective methodology that can systematically identify the functional interaction structure of a gene network from time-series expression profiles. In particular, we need to take into account the different time delay effects in gene regulation since they are ubiquitously present. We have considered a new experiment that measures the overall expression changes after a perturbation on a specific gene. Based on this experiment, we have proposed a new inference method that can take account of the time delay induced while the perturbation affects its primary target genes. Specifically, we have developed an algebraic equation from which we can identify the subnetwork structure around the perturbed gene. We have also analyzed the influence of time delay on the inferred network structure. The proposed method is particularly useful for identification of a gene network with small variations in the time delay of gene regulation.
机译：仅从诸如结合基序之类的序列信息推断基因（调控）网络的功能相互作用结构方面存在基本限制。为了克服这些限制，已经开发了各种方法来从表达谱中推断功能相互作用结构。然而，由于实验的局限性和计算复杂性，它们中的大多数都没有那么成功。因此，迫切需要开发一种简单但有效的方法，该方法可从时序表达谱系统地鉴定基因网络的功能相互作用结构。特别是，我们需要考虑基因调控中不同的时延效应，因为它们无处不在。我们考虑了一项新的实验，该实验测量对特定基因产生干扰后的整体表达变化。基于此实验，我们提出了一种新的推断方法，该方法可以考虑扰动影响其主要目标基因时引起的时间延迟。具体来说，我们已经开发了一个代数方程，从中我们可以确定扰动基因周围的子网结构。我们还分析了时间延迟对推断网络结构的影响。所提出的方法对于鉴定基因调控的时间延迟具有很小变化的基因网络特别有用。

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