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首页> 外文会议>Bioinformatics Research and Applications; Lecture Notes in Bioinformatics; 4463 >Comparative Analysis of Gene-Coexpression Networks Across Species
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Comparative Analysis of Gene-Coexpression Networks Across Species

机译：跨物种的基因共表达网络的比较分析

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This paper presents a large scale analysis of gene-coexpression networks (GCNs) across four plant species, I.e. Arabidopsis, Barley, Soybean, and Wheat, over 1471 DNA microarrays. We first identify a set of 5164 metagenes that are highly conserved across all of them. For each of the four species, a GCN is constructed by linking reliable coexpressed metagene pairs based on their expression profiles within each species. Similarly, an overall GCN for the four species is constructed based on gene expression profiles across the four species. On average, more than 50K correlation links have been generated for each of the five networks. A number of recent studies have shown that topological structures of GCNs and some other biological networks have some common characteristics, and GCNs across species may reveals conserved genetic modules that contain functionally related genes. But no studies on GCNs across crop species have been reported. In this study, we focus on the comparative analysis of statistical properties on the topological structure of the above five networks across Arabidopsis and three crop species. We show that: (1) the five networks are scale-free and their degree distributions follow the power law; (2) these networks have the small-world property; (3) these networks share very similar values for a variety of network parameters such as degree distributions, network diameters, cluster coefficients, and frequency distributions of correlation patterns (sub-graphs); (4) these networks are non-random and are stable; (5) cliques and clique-like subgraphs are overly present in these networks. Further analysis can be carried out to investigate conserved functional modules and regulatory pathways across the four species based on these networks. A web-based computing tool, available at http://cbc.case.edu/coexp.html, has been designed to visualize expression profiles of metagenes across the four species.
机译：本文介绍了跨四种植物物种的基因共表达网络（GCN）的大规模分析。超过1471个DNA芯片的拟南芥，大麦，大豆和小麦。我们首先确定一组5164个基因，它们在所有基因中高度保守。对于这四个物种中的每个物种，都基于它们在每个物种中的表达谱，通过连接可靠的共表达元基因对来构建GCN。同样，基于四个物种的基因表达谱，构建了四个物种的整体GCN。平均而言，五个网络中的每个网络都生成了超过5万个相关链接。最近的许多研究表明，GCN和其他一些生物网络的拓扑结构具有某些共同特征，跨物种的GCN可能揭示了保守的遗传模块，这些模块包含功能相关的基因。但是，没有关于跨农作物物种的GCN的研究的报道。在这项研究中，我们专注于对拟南芥和三种农作物物种的上述五个网络的拓扑结构统计特性的比较分析。我们证明：（1）这五个网络是无尺度的，它们的度分布遵循幂定律； （2）这些网络具有小世界性质； （3）这些网络对于各种网络参数（例如度分布，网络直径，簇系数和相关模式的频率分布（子图））共享非常相似的值； （4）这些网络是非随机且稳定的； （5）在这些网络中过多存在集团和类似集团的子图。基于这些网络，可以进行进一步的分析以研究跨越四个物种的保守功能模块和调控途径。一种基于Web的计算工具，可从http://cbc.case.edu/coexp.html获得，旨在可视化跨越这四个物种的基因表达谱。

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