eRNA-IDO:A One-stop Platform for Identification,Interactome Discovery,and Functional Annotation of Enhancer RNAs  

作　　者：Yuwei Zhang Lihai Gong Ruofan Ding Wenyan Chen Hao Rong Yanguo Li Fawziya Shameem Korakkandan Arshad Ali Lei Li Qi Liao 

机构地区：[1]School of Public Health,Health Science Center,Ningbo University,Ningbo 315211,China [2]Biomedical Big Data Center,the First Affiliated Hospital,Zhejiang University School of Medicine,Hangzhou 310003,China [3]Institute of Systems and Physical Biology,Shenzhen Bay Laboratory,Shenzhen 518107,China [4]School of Clinical Medicine,Health Science Center,Ningbo University,Ningbo 315211,China [5]Institute of Drug Discovery Technology,Ningbo University,Ningbo 315211,China

出　　处：《Genomics, Proteomics & Bioinformatics》2024年第4期169-179,共11页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant Nos.32300430,32100533,and 31970630);the Open Grant Funds from Shenzhen Bay Laboratory(Grant No.SZBL2021080601001 to Lei Li);the Zhejiang Provincial Natural Science Foundation of China(Grant No.LY21C060002);the Ningbo Major Research and Development Plan Project(Grant Nos.2023Z226 and 2023Z171),China.

摘　　要：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 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/.

关 键 词：Enhancer RNA IDENTIFICATION INTERACTOME Functional annotation Web server 

分 类 号：Q78[生物学—分子生物学]