植物PAN 4.0:更新了数据库,用于识别保存的非编码序列,并探索植物促进剂的动态转录调节
Chi-Nga Chow1,2, Chien-Wen Yang1, Nai-Yun Wu1
1Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan.
Nucleic acids research
|October 28, 2023
概括
植物PAN 4.0增强了115个物种的植物转录监管网络建设. 此更新的资源有助于识别保存的非编码序列,并分析 cis-regulatory 元素的演变.
科学领域:
- 植物生物学 植物生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 转录调节网络 (TRNs) 对于理解植物的基因表达至关重要.
- 工厂TRN建设的现有资源需要扩展,以覆盖更多的物种和数据类型.
研究的目的:
- 更新和扩展PlantPAN,这是工厂TRN建设的整合性资源.
- 增强分析 cis 调节元素和在植物物种中保存的非编码序列的能力.
主要方法:
- 扩展了115种植物物种的基因注释和促进子序列.
- 更新了转录因子结合站点存储库,为18305个转录因子提供了3428个矩阵.
- 整合了调控因子基因组景观的手动更新,并添加了来自Chlamydomonas reinhardtii的ChIP-seq数据.
主要成果:
- 植物PAN 4.0 现在支持 115 种物种的 TRN 构造,方便对 cis 调节元素的进化比较.
- 在同源基因中改进了保存的非编码序列的识别.
- 对ChIP-seq数据的增强分析工具,包括实验条件集群和基因本体学丰富,提供了更清晰的见解.
结论:
- 植物PAN 4.0是一个全面的资源,用于重建植物基因调节网络.
- 更新后的系统可以有效地比较跨物种和实验的基因组 cis-regulatory 元素.
- 促进对植物基因调节,进化和保护的研究.
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