PlantGSAD: a comprehensive gene set annotation database for plant species.
PlantGSAD: a comprehensive gene set annotation database for plant species.
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PlantGSAD：植物物种综合基因集注释数据库
DOI：
10.1093/nar/gkab794
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发表时间：
2022-01-07
影响因子：
14.9
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
Ma X;Yan H;Yang J;Liu Y;Li Z;Sheng M;Cao Y;Yu X;Yi X;Xu W;Su Z
摘要 随着高通量实验海量数据集的积累和新型组学数据的迅速出现，基因集变得更加多样化，对于多维水平的基因注释细化至关重要。因此，我们在植物基因集注释数据库 (PlantGSAD) 中收集并定义了 44 个植物物种不同类别的 236 007 个基因集。这些基因集分为九个主要类别，涵盖许多功能子类别，例如性状本体、共表达模块、染色质状态和液-液相分离。 The annotations from the collected gene sets covered all of the genes in the Brassicaceae species Arabidopsis and Poaceae species Oryza sativa. PlantGSAD 中实现了多种 GSEA 工具来提高分析效率，包括基于自定义注释的灵活策略的定制 SEA、用于 SEA 结果交叉比较的 SEACOMPARE，以及用于直观反映其父子关系的本体分析的集成可视化功能。 In summary, PlantGSAD provides numerous gene sets for multiple plant species and highly efficient analysis tools.我们相信PlantGSAD将成为一个多功能分析平台，可用于预测和阐明感兴趣基因的功能和机制。 PlantGSAD is publicly available at http://systemsbiology.cau.edu.cn/PlantGSEAv2/.
Abstract With the accumulation of massive data sets from high-throughput experiments and the rapid emergence of new types of omics data, gene sets have become more diverse and essential for the refinement of gene annotation at multidimensional levels. Accordingly, we collected and defined 236 007 gene sets across different categories for 44 plant species in the Plant Gene Set Annotation Database (PlantGSAD). These gene sets were divided into nine main categories covering many functional subcategories, such as trait ontology, co-expression modules, chromatin states, and liquid-liquid phase separation. The annotations from the collected gene sets covered all of the genes in the Brassicaceae species Arabidopsis and Poaceae species Oryza sativa. Several GSEA tools are implemented in PlantGSAD to improve the efficiency of the analysis, including custom SEA for a flexible strategy based on customized annotations, SEACOMPARE for the cross-comparison of SEA results, and integrated visualization features for ontological analysis that intuitively reflects their parent-child relationships. In summary, PlantGSAD provides numerous gene sets for multiple plant species and highly efficient analysis tools. We believe that PlantGSAD will become a multifunctional analysis platform that can be used to predict and elucidate the functions and mechanisms of genes of interest. PlantGSAD is publicly available at http://systemsbiology.cau.edu.cn/PlantGSEAv2/.
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