Dipartimento di Biologia Ecologia e Scienze della Terra, Università della Calabria, Rende 87036, Italy.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK.
Database (Oxford). 2023 Oct 11;2023. doi: 10.1093/database/baad066.
In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on ncRNA functional and physical associations. In the present paper, we present a collection of microRNA-mRNA interactions annotated from the scientific literature following recognized standard criteria and focused on microRNAs, which regulate genes associated with rare diseases as a case study. The list of protein-coding genes with a known role in specific rare diseases was retrieved from the Genome England PanelApp, and associated microRNA-mRNA interactions were annotated in the IntAct database and compared with other datasets. RNAcentral identifiers were used for unambiguous, stable identification of ncRNAs. The information about the interaction was enhanced by a detailed description of the cell types and experimental conditions, providing a computer-interpretable summary of the published data, integrated with the huge amount of protein interactions already gathered in the database. Furthermore, for each interaction, the binding sites of the microRNA are precisely mapped on a well-defined mRNA transcript of the target gene. This information is crucial to conceive and design optimal microRNA mimics or inhibitors to interfere in vivo with a deregulated process. As these approaches become more feasible, high-quality, reliable networks of microRNA interactions are needed to help, for instance, in the selection of the best target to be inhibited and to predict potential secondary off-target effects. Database URL https://www.ebi.ac.uk/intact.
近年来，科学文献和数据库中描述了大量关于 ncRNA 相互作用的数据。尽管已经做出了相当大的努力来注释公共存储库中可用的知识，但不同资源在捕捉和解释 ncRNA 功能和物理关联数据方面仍然存在很大差异。在本文中，我们展示了根据公认标准从科学文献中注释的 microRNA-mRNA 相互作用的集合，重点是作为案例研究的调节与罕见疾病相关基因的 microRNA。具有已知在特定罕见疾病中作用的蛋白质编码基因列表是从 Genome England PanelApp 中检索到的，并且在 IntAct 数据库中注释了相关的 microRNA-mRNA 相互作用，并与其他数据集进行了比较。RNAcentral 标识符用于对 ncRNA 进行明确、稳定的识别。通过详细描述细胞类型和实验条件来增强有关相互作用的信息，为已发布数据提供了计算机可解释的摘要，与数据库中已经收集的大量蛋白质相互作用进行了集成。此外，对于每个相互作用，microRNA 的结合位点都精确地映射到目标基因的明确定义的 mRNA 转录本上。该信息对于设计最佳 microRNA 模拟物或抑制剂以在体内干扰失调过程至关重要。随着这些方法变得更加可行，需要高质量、可靠的 microRNA 相互作用网络来帮助选择要抑制的最佳靶标，并预测潜在的次要脱靶效应。数据库网址 https://www.ebi.ac.uk/intact.
