聚合的基因共同表达网络预测了葡萄藤中的转录因子调节景观
Luis Orduña1, Antonio Santiago1, David Navarro-Payá1
1Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain.
Journal of experimental botany
|September 5, 2023
概括
聚合基因共同表达网络 (aggGCNs) 揭示了葡萄藤中强大的相互作用. 这种方法成功地确定了转录因子的已知和新型调节作用,有助于理解植物代谢途径.
科学领域:
- 植物基因组学 植物基因组学
- 生物信息学是一种生物信息学.
- 系统生物学 系统生物学
背景情况:
- 在非模型植物中,基因共同表达网络 (GCN) 尚未得到充分探索.
- 转录组数据的积累为网络分析提供了机会.
- 聚合GCNs (聚合GCNs) 增强了强大的共同表达相互作用和功能连接的检测.
研究的目的:
- 使用公开的RNA-Seq数据,应用和评估葡萄藤中GCN的两个聚合方法.
- 调查aggGCNs在识别转录因子基因家族的调控关系中的实用性.
- 探索转录因子在葡萄藤代谢途径中的新型调节作用.
主要方法:
- 将两种基因网络聚合方法应用于葡萄树叶,果和所有器官的葡萄树RNA-Seq数据集.
- 利用基于同时发生的聚合,将其确定为高性能方法.
- 进行了转录因子和路径中心网络分析.
主要成果:
- 基于同时发生的聚合产生了最有效的葡萄藤网络.
- 确定了R2R3-MYB,bHLH/MYC转录因子和代谢途径之间的已知和新的调节联系.
- 验证的aggGCNs作为基因调控网络的代理,使用DNA亲和力净化测序数据.
结论:
- 聚合的GCN对研究非模型植物 (如葡萄藤) 的基因调节有效.
- 阐明了VviMYBPA1在益西安丁积累和p-coumaroyl-CoA生物合成中的作用.
- 这项研究提供了一个可复制的网络存储库和Vitviz平台,用于探索葡萄树的共同表达.
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