Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data
Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data
复制标题
植物调节组学：数据驱动的接口，用于从植物多组学数据中检索上游调节剂
DOI：
10.1111/tpj.14526
复制
发表时间：
2020-01-01
期刊：
影响因子：
7.2
通讯作者：
Zhang, Yijing
中科院分区：
文献类型：
--
作者：
Ran, Xiaojuan;Zhao, Fei;Zhang, Yijing
高通量技术已成为常规植物研究的有力手段。解释高通量数据的生物学意义主要集中在一个大的基因列表或基因组位点的功能表征，涉及以下两个方面：基因或位点的功能和它们是如何作为一个整体进行调控的，即寻找上游调控因子。传统的功能注释平台在很大程度上有助于解决第一个问题。解决第二个问题对于全球了解监管机制至关重要，但更具挑战性，需要更多的高通量实验证据和统一的数据挖掘统计框架。组学数据的快速积累提供了大量的实验数据。我们在这里提出植物Regulomics，一个接口，集成了19 925转录组和表观基因组数据集和不同来源的功能证据（58 112条款和695 414蛋白质-蛋白质相互作用）从6种植物沿着与56个全基因组测序的植物物种的直向同源基因。在同一研究中进行具有生物学意义的所有成对转录组学比较，并且将所有表观基因组数据处理为由各种因素靶向的基因组基因座。这些数据被很好地组织到基因模块和位点列表中，这些模块和位点列表被进一步实施到相同的统计框架中。对于任何输入基因列表或基因组位点，Plant Regulomics从整合的组学数据中检索调节输入的上游因子、处理和实验/环境条件。此外，通过用户友好的网络界面提供多种工具和交互式可视化。Plant Regulomics可在.
High-throughput technology has become a powerful approach for routine plant research. Interpreting the biological significance of high-throughput data has largely focused on the functional characterization of a large gene list or genomic loci that involves the following two aspects: the functions of the genes or loci and how they are regulated as a whole, i.e. searching for the upstream regulators. Traditional platforms for functional annotation largely help resolving the first issue. Addressing the second issue is essential for a global understanding of the regulatory mechanism, but is more challenging, and requires additional high-throughput experimental evidence and a unified statistical framework for data-mining. The rapid accumulation of 'omics data provides a large amount of experimental data. We here present Plant Regulomics, an interface that integrates 19 925 transcriptomic and epigenomic data sets and diverse sources of functional evidence (58 112 terms and 695 414 protein-protein interactions) from six plant species along with the orthologous genes from 56 whole-genome sequenced plant species. All pair-wise transcriptomic comparisons with biological significance within the same study were performed, and all epigenomic data were processed to genomic loci targeted by various factors. These data were well organized to gene modules and loci lists, which were further implemented into the same statistical framework. For any input gene list or genomic loci, Plant Regulomics retrieves the upstream factors, treatments, and experimental/environmental conditions regulating the input from the integrated 'omics data. Additionally, multiple tools and an interactive visualization are available through a user-friendly web interface. Plant Regulomics is available at .