越来越多的证据支持增强子 RNA (eRNA) 的转录及其在基因调控中的重要作用。然而，它们与其他生物分子的相互作用及其相应的功能仍然知之甚少。为了促进机制研究，本研究提出了 eRNA-IDO，这是第一个用于人类 eRNA 识别、相互作用组发现和功能注释的综合计算平台。 eRNA-IDO 包含两个模块：eRNA-ID 和 eRNA-Anno。从功能上讲，eRNA-ID 可以从头组装的转录组中识别 eRNA。 eRNA-ID包含8种增强子生成器，使用户能够灵活方便地定制增强子区域。此外，eRNA-Anno 通过分析 eRNA 与编码基因之间预先构建或用户定义的网络的 eRNA 相互作用组，为新的和已知的 eRNA 提供细胞特异性/组织特异性功能注释。预构建的网络包括正常组织中基于基因型组织表达（GTEx）的共表达网络、癌症组织中基于癌症基因组图谱（TCGA）的共表达网络以及基于组学的以 eRNA 为中心的调控网络。 eRNA-IDO 可以促进 eRNA 的生物发生和功能的研究。 eRNA-IDO 服务器可在 http://bioinfo.szbl.ac.cn/eRNA_IDO/ 上免费获取。© 作者 2024。由牛津大学出版社和科学出版社代表北京基因组研究所出版中国科学院/中国国家生物信息与遗传学中心。

Growing evidence supports the transcription of enhancer RNAs (eRNAs) and their important roles in gene regulation. However, their interactions with other biomolecules and their corresponding functionality remain poorly understood. In an attempt to facilitate mechanistic research, this study presents eRNA-IDO, the first integrative computational platform for the identification, interactome discovery, and functional annotation of human eRNAs. eRNA-IDO comprises two modules: eRNA-ID and eRNA-Anno. Functionally, eRNA-ID can identify eRNAs from de novo assembled transcriptomes. eRNA-ID includes 8 kinds of enhancer makers, enabling users to customize enhancer regions flexibly and conveniently. In addition, eRNA-Anno provides cell-specific/tissue-specific functional annotation for both new and known eRNAs by analyzing the eRNA interactome from prebuilt or user-defined networks between eRNA and coding gene. The prebuilt networks include the Genotype-Tissue Expression (GTEx)-based co-expression networks in normal tissues, The Cancer Genome Atlas (TCGA)-based co-expression networks in cancer tissues, and omics-based eRNA-centric regulatory networks. eRNA-IDO can facilitate research on the biogenesis and functions of eRNAs. The eRNA-IDO server is freely available at http://bioinfo.szbl.ac.cn/eRNA_IDO/.© The Author(s) 2024. Published by Oxford University Press and Science Press on behalf of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.