Precedence Temporal Networks to represent temporal relationships in gene expression data
Precedence Temporal Networks to represent temporal relationships in gene expression data
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DOI：
10.1016/j.jbi.2007.06.003
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发表时间：
2007-12-01
影响因子：
4.5
通讯作者：
Bellazzi, Riccardo
中科院分区：
文献类型：
--
作者：
Sacchi, Lucia;Larizza, Cristiana;Bellazzi, Riccardo
从基因表达时间序列重建基因调控网络是目前一个有趣的研究挑战。在这种分析的一个关键问题是自动提取的优先级和基因之间的同步假设随着时间的推移，目前的工作介绍了优先时序网络（PTN），一种新的方法来提取和可视化基因之间的时间关系。PTNs是一种特殊的时间网络，其中节点代表时间模式，而边缘识别节点之间的优先或同步关系。该方法在两个案例studies.The测试：表达的一个子集的基因在土壤变形虫Dictyosteelium discoideum和一组充分研究的基因参与人类细胞周期调控。所提取的网络反映了该算法清楚地重建所考虑的基因集的时间的能力，分别突出显示了网骨藻发育和细胞周期的不同阶段。(C)2007年爱思唯尔公司All rights reserved.
The reconstruction of gene regulatory networks from gene expression time series is nowadays an interesting research challenge. A key problem in this kind of analysis is the automated extraction of precedence and synchronization between interesting patterns assumed by genes over time.The present work introduces Precedence Temporal Networks (PTN), a novel method to extract and visualize temporal relationships between genes. PTNs are a special kind of temporal network where nodes represent temporal patterns while edges identify precedence or synchronization relationships between the nodes.The method is tested on two case studies: the expression of a subset of genes in the soil amoeba Dictyostelium discoideum and of a set of well-studied genes involved in the human cell cycle regulation. The extracted networks reflect the capability of the algorithm to clearly reconstruct the timing of the considered gene sets, highlighting different stages in Dictyostelium development and in the cell cycle, respectively. (C) 2007 Elsevier Inc. All rights reserved.