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Inferring gene regulatory networks from gene expression data by a dynamic Bayesian network-based model

机译:通过基于动态贝叶斯网络的模型从基因表达数据推断基因调控网络

摘要

Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the efficiency of DBN in inferring GRNs is often hampered by missing values in expression data, and excessive computation time due to the large search space whereby DBN treats all genes as potential regulators for a target gene. In this paper, we proposed a DBN-based model with missing values imputation to improve inference efficiency, and potential regulators detection which aims to lessen computation time by limiting potential regulators based on expression changes. The performance of the proposed model is assessed by using time-series expression data of yeast cell cycle. The experimental results showed reduced computation time and improved efficiency in detecting gene-gene relationships.
机译:由于生物信息学的最新进展,从基因表达数据推断基因调控网络(GRN)引起了研究人员的极大兴趣。这是由于研究人员需要了解动态行为并发现网络中隐藏的大量信息。在这方面,由于动态贝叶斯网络(DBN)具有处理时间序列微阵列数据和建模反馈回路的能力,因此被广泛地用于推断GRN。但是,DBN推断GRN的效率通常受到表达数据缺失值的困扰,并且由于搜索空间大而导致计算时间过长,DBN将所有基因都视为靶基因的潜在调控因子。在本文中,我们提出了一种基于DBN的模型,该模型具有缺失值插补功能以提高推理效率,并提出了潜在的调节子检测方法,旨在通过基于表达式变化限制潜在的调节子来减少计算时间。通过使用酵母细胞周期的时间序列表达数据评估提出的模型的性能。实验结果表明,减少了计算时间,提高了检测基因与基因关系的效率。

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