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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 eight kinds of enhancer makers, enabling users to customize enhancer regions flexibly and conveniently. In addition, eRNA-Anno provides cell-\/tissue-specific functional annotation for both new and known eRNAs by analyzing the eRNA interactome from prebuilt or user-defined networks between eRNAs and protein-coding genes. 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\/.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae059","type":"journal-article","created":{"date-parts":[[2024,8,23]],"date-time":"2024-08-23T20:29:13Z","timestamp":1724444953000},"source":"Crossref","is-referenced-by-count":5,"title":["eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8395-3020","authenticated-orcid":false,"given":"Yuwei","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","place":["China"]},{"name":"Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 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