Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum.
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum.
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共表达网络分析确定了与树木发育和应激反应相关的功能模块
DOI：
10.1038/srep38436
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发表时间：
2016-12-06
影响因子：
4.6
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
You Q;Zhang L;Yi X;Zhang K;Yao D;Zhang X;Wang Q;Zhao X;Ling Y;Xu W;Li F;Su Z
棉花是一种重要的经济作物，对农业和纺织业至关重要。通过整合转录组数据，我们发现多维共表达网络分析对于预测棉花基因功能和功能模块非常有效。在这里，利用最近获得的树棉转录组数据，包括组织和应激处理样本的多个生长阶段的数据，构建了一个共表达网络，通过多层方法探索多维表达（发育和应激）。基于差异基因表达和网络分析，发现基因GaKNL1的纤维发育调节模块通过抑制REVOLUTA的活性来调节第二细胞壁，并检查了GaJAZ1a的组织选择性模块对水分胁迫的响应。此外，JAZ1相关调控模块的比较基因组学分析揭示了植物物种之间的高度保守性。此外，通过整合共表达网络、模块分类和功能富集工具，识别出1155个功能模块，涵盖代谢、应激反应、转录调控等功能。最终建立了网络分析在线平台（http://structuralbiology.cau.edu.cn/arboreum），有助于细化棉花基因功能注释，建立数据挖掘系统，识别具有重要农艺性状的功能基因或模块。
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches. Based on differential gene expression and network analysis, a fibre development regulatory module of the gene GaKNL1 was found to regulate the second cell wall through repressing the activity of REVOLUTA, and a tissue-selective module of GaJAZ1a was examined in response to water stress. Moreover, comparative genomics analysis of the JAZ1-related regulatory module revealed high conservation across plant species. In addition, 1155 functional modules were identified through integrating the co-expression network, module classification and function enrichment tools, which cover functions such as metabolism, stress responses, and transcriptional regulation. In the end, an online platform was built for network analysis (http://structuralbiology.cau.edu.cn/arboreum), which could help to refine the annotation of cotton gene function and establish a data mining system to identify functional genes or modules with important agronomic traits.
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