National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
Nucleic Acids Res. 2021 Jul 2;49(W1):W523-W529. doi: 10.1093/nar/gkab383.
Characterizing regulatory effects of genomic variants in plants remains a challenge. Although several tools based on deep-learning models and large-scale chromatin-profiling data have been available to predict regulatory elements and variant effects, no dedicated tools or web services have been reported in plants. Here, we present PlantDeepSEA as a deep learning-based web service to predict regulatory effects of genomic variants in multiple tissues of six plant species (including four crops). PlantDeepSEA provides two main functions. One is called Variant Effector, which aims to predict the effects of sequence variants on chromatin accessibility. Another is Sequence Profiler, a utility that performs 'in silico saturated mutagenesis' analysis to discover high-impact sites (e.g., cis-regulatory elements) within a sequence. When validated on independent test sets, the area under receiver operating characteristic curve of deep learning models in PlantDeepSEA ranges from 0.93 to 0.99. We demonstrate the usability of the web service with two examples. PlantDeepSEA could help to prioritize regulatory causal variants and might improve our understanding of their mechanisms of action in different tissues in plants. PlantDeepSEA is available at http://plantdeepsea.ncpgr.cn/.
鉴定植物基因组变异的调控效应仍然是一个挑战。尽管已经有几种基于深度学习模型和大规模染色质分析数据的工具可用于预测调控元件和变异效应，但在植物中尚未报道专门的工具或网络服务。在这里，我们提出了 PlantDeepSEA，这是一个基于深度学习的网络服务，可预测六个植物物种（包括四种作物）的多个组织中基因组变异的调控效应。PlantDeepSEA 提供了两个主要功能。一个称为 Variant Effector，旨在预测序列变异对染色质可及性的影响。另一个是 Sequence Profiler，这是一种实用程序，可进行“计算机饱和诱变分析”，以发现序列内的高影响位点（例如顺式调控元件）。在独立的测试集上进行验证时，PlantDeepSEA 中深度学习模型的接收器操作特征曲线下面积范围为 0.93 到 0.99。我们通过两个示例展示了该网络服务的可用性。PlantDeepSEA 可以帮助优先考虑调控因果变异，并可能有助于我们理解它们在植物不同组织中的作用机制。PlantDeepSEA 可在 http://plantdeepsea.ncpgr.cn/ 上获得。
