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/.

中文翻译：

---

PlantGSAD：植物物种综合基因集注释数据库

随着来自高通量实验的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，对于在多维水平上细化基因注释至关重要。因此，我们在植物基因集注释数据库 (PlantGSAD) 中为 44 个植物物种收集并定义了 236 007 个不同类别的基因集。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。来自收集的基因集的注释涵盖了十字花科物种拟南芥和禾本科物种水稻中的所有基因。PlantGSAD 中实施了几个 GSEA 工具以提高分析效率，包括用于基于自定义注释的灵活策略的自定义 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。总之，PlantGSAD 为多种植物物种提供了大量基因组和高效的分析工具。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 可在 http://systemsbiology.cau.edu.cn/PlantGSEAv2/ 上公开获得。PlantGSAD 为多种植物物种和高效的分析工具提供了大量的基因集。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 可在 http://systemsbiology.cau.edu.cn/PlantGSEAv2/ 上公开获得。PlantGSAD 为多种植物物种和高效的分析工具提供了大量的基因集。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 可在 http://systemsbiology.cau.edu.cn/PlantGSEAv2/ 上公开获取。