尽管已鉴定出 170 多种化学修饰，但它们的普遍性、机制和功能仍然很大程度上未知。为了实现对不同RNA修饰谱的综合分析，我们开发了RBase v3.0（http:////bioinformaticsscience.cn//rmbase//），这是一个由八个模块组成的综合平台。这些模块有助于探索转录组范围内的景观、生物发生、相互作用组和 RNA 修饰的功能。通过利用新颖的流程挖掘数千个表观转录组数据集，“RNA 修饰”模块揭示了 62 个物种的 73 个 RNA 修饰图谱。 “基因”模块允许通过基因和转录本检索 RNA 修饰谱和簇。 “机制”模块探索 23,382 个酶催化或 snoRNA 引导的修饰位点，以阐明其生物发生机制。 “共定位”模块系统地阐述了各种细胞系中 14 个组蛋白修饰和 6 个 RNA 修饰之间的潜在相关性。 “RMP”模块研究 18 种癌症中 146 种 RNA 修饰蛋白 (RMP) 的差异表达谱。 “Interactome”整合了 73 个 RNA 修饰与 RBP 结合事件、miRNA 靶标和 SNP 之间的相互作用关系。 “Motif”阐明了从表观转录组数据集中识别出的 11 种 RNA 修饰的丰富基序。 “工具”引入了一种新颖的基于网络的“modGeneTool”，用于注释修改。总体而言，RBase v3.0 提供了用于研究 RNA 修饰的各种资源和工具。© 作者 2023。由牛津大学出版社代表 Nucleic Acids Research 出版。

Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http:////bioinformaticsscience.cn//rmbase//), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the 'RNA Modifications' module reveals the map of 73 RNA modifications of 62 species. the 'Genes' module allows to retrieve RNA modification profiles and clusters by gene and transcript. The 'Mechanisms' module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The 'Co-localization' module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The 'RMP' module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The 'Interactome' integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The 'Motif' illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The 'Tools' introduces a novel web-based 'modGeneTool' for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.