{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T17:34:14Z","timestamp":1775756054881,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,8,13]],"date-time":"2021-08-13T00:00:00Z","timestamp":1628812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31822030"],"award-info":[{"award-number":["31822030"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31801113"],"award-info":[{"award-number":["31801113"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31801154"],"award-info":[{"award-number":["31801154"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771458"],"award-info":[{"award-number":["31771458"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2019M652623"],"award-info":[{"award-number":["2019M652623"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2018M632830"],"award-info":[{"award-number":["2018M632830"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2017M622455"],"award-info":[{"award-number":["2017M622455"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2019T120664"],"award-info":[{"award-number":["2019T120664"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Extracellular vesicles (EVs) packing various molecules play vital roles in intercellular communication. Non-coding RNAs (ncRNAs) are important functional molecules and biomarkers in EVs. A comprehensive investigation of ncRNAs expression in EVs under different conditions is a fundamental step for functional discovery and application of EVs. Here, we curated 2030 small RNA-seq datasets for human EVs (1506 sEV and 524 lEV) in 24 conditions and over 40 diseases. We performed a unified reads dynamic assignment algorithm (RDAA) considering mismatch and multi-mapping reads to quantify the expression profiles of seven ncRNA types (miRNA, snoRNA, piRNA, snRNA, rRNA, tRNA and Y RNA). We constructed EVAtlas (http:\/\/bioinfo.life.hust.edu.cn\/EVAtlas), a comprehensive database for ncRNA expression in EVs with four functional modules: (i) browse and compare the distribution of ncRNAs in EVs from 24 conditions and eight sources (plasma, serum, saliva, urine, sperm, breast milk, primary cell and cell line); (ii) prioritize candidate ncRNAs in condition related tissues based on their expression; (iii) explore the specifically expressed ncRNAs in EVs from 24 conditions; (iv) investigate ncRNA functions, related drugs, target genes and EVs isolation methods. EVAtlas contains the most comprehensive ncRNA expression in EVs and will be a key resource in this field.<\/jats:p>","DOI":"10.1093\/nar\/gkab668","type":"journal-article","created":{"date-parts":[[2021,7,23]],"date-time":"2021-07-23T11:13:58Z","timestamp":1627038838000},"page":"D111-D117","source":"Crossref","is-referenced-by-count":60,"title":["EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3008-3375","authenticated-orcid":false,"given":"Chun-Jie","family":"Liu","sequence":"first","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan\u00a0430074, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2924-5306","authenticated-orcid":false,"given":"Gui-Yan","family":"Xie","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan\u00a0430074, China"}]},{"given":"Ya-Ru","family":"Miao","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan\u00a0430074, China"}]},{"given":"Mengxuan","family":"Xia","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan\u00a0430074, China"}]},{"given":"Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan\u00a0430074, China"}]},{"given":"Qian","family":"Lei","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan\u00a0430074, China"}]},{"given":"Qiong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong\u00a0226001, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5099-7465","authenticated-orcid":false,"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan\u00a0430074, China"},{"name":"Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong\u00a0226001, China"}]}],"member":"286","published-online":{"date-parts":[[2021,8,13]]},"reference":[{"key":"2022010507395459800_B1","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1016\/j.cell.2016.01.043","article-title":"Communication by extracellular vesicles: where we are and where we need to go","volume":"164","author":"Tkach","year":"2016","journal-title":"Cell"},{"key":"2022010507395459800_B2","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1083\/jcb.201211138","article-title":"Extracellular vesicles: exosomes, microvesicles, and friends","volume":"200","author":"Raposo","year":"2013","journal-title":"J. Cell Biol."},{"key":"2022010507395459800_B3","doi-asserted-by":"crossref","first-page":"1535750","DOI":"10.1080\/20013078.2018.1535750","article-title":"Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines","volume":"7","author":"Th\u00e9ry","year":"2018","journal-title":"J. Extracell. Vesicles"},{"key":"2022010507395459800_B4","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/s41571-018-0036-9","article-title":"Extracellular vesicles in cancer \u2013 implications for future improvements in cancer care","volume":"15","author":"Xu","year":"2018","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"2022010507395459800_B5","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41580-020-0251-y","article-title":"RNA delivery by extracellular vesicles in mammalian cells and its applications","volume":"21","author":"O\u2019Brien","year":"2020","journal-title":"Nat. Rev. Mol. Cell. Biol."},{"key":"2022010507395459800_B6","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/nature15756","article-title":"Tumour exosome integrins determine organotropic metastasis","volume":"527","author":"Hoshino","year":"2015","journal-title":"Nature"},{"key":"2022010507395459800_B7","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/j.cell.2019.02.029","article-title":"Reassessment of exosome composition","volume":"177","author":"Jeppesen","year":"2019","journal-title":"Cell"},{"key":"2022010507395459800_B8","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/j.cell.2019.10.017","article-title":"The role of non-coding RNAs in oncology","volume":"179","author":"Slack","year":"2019","journal-title":"Cell"},{"key":"2022010507395459800_B9","doi-asserted-by":"crossref","first-page":"5228","DOI":"10.1038\/s41467-018-07657-1","article-title":"Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors","volume":"9","author":"Dhawan","year":"2018","journal-title":"Nat. Commun."},{"key":"2022010507395459800_B10","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1038\/nrc3195","article-title":"Are snoRNAs and snoRNA host genes new players in cancer","volume":"12","author":"Williams","year":"2012","journal-title":"Nat. Rev. Cancer"},{"key":"2022010507395459800_B11","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1016\/j.cell.2016.05.046","article-title":"Modulated expression of specific tRNAs drives gene expression and cancer progression","volume":"165","author":"Goodarzi","year":"2016","journal-title":"Cell"},{"key":"2022010507395459800_B12","doi-asserted-by":"crossref","first-page":"1968","DOI":"10.1016\/j.celrep.2017.10.070","article-title":"A Pan-cancer analysis of the expression and clinical relevance of small nucleolar RNAs in human cancer","volume":"21","author":"Gong","year":"2017","journal-title":"Cell Rep."},{"key":"2022010507395459800_B13","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1080\/15476286.2019.1657744","article-title":"tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers","volume":"17","author":"Zhang","year":"2019","journal-title":"RNA Biol."},{"key":"2022010507395459800_B14","doi-asserted-by":"crossref","first-page":"D89","DOI":"10.1093\/nar\/gky985","article-title":"EVmiRNA: a database of miRNA profiling in extracellular vesicles","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507395459800_B15","doi-asserted-by":"crossref","first-page":"202","DOI":"10.3389\/fimmu.2019.00202","article-title":"Transcriptome of extracellular vesicles: State-of-the-Art","volume":"10","author":"Turchinovich","year":"2019","journal-title":"Front. Immunol."},{"key":"2022010507395459800_B16","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1038\/s41467-017-01196-x","article-title":"Coding and noncoding landscape of extracellular RNA released by human glioma stem cells","volume":"8","author":"Wei","year":"2017","journal-title":"Nat Commun."},{"key":"2022010507395459800_B17","doi-asserted-by":"crossref","first-page":"415","DOI":"10.3389\/fphar.2018.00415","article-title":"Extracellular vesicles as carriers of non-coding RNAs in liver diseases","volume":"9","author":"Yang","year":"2018","journal-title":"Front. Pharmacol."},{"key":"2022010507395459800_B18","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1016\/j.jmb.2015.09.019","article-title":"ExoCarta: a web-based compendium of exosomal cargo","volume":"428","author":"Keerthikumar","year":"2016","journal-title":"J. Mol. Biol."},{"key":"2022010507395459800_B19","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1093\/bioinformatics\/btu741","article-title":"EVpedia: a community web portal for extracellular vesicles research","volume":"31","author":"Kim","year":"2015","journal-title":"Bioinformatics"},{"key":"2022010507395459800_B20","doi-asserted-by":"crossref","first-page":"D516","DOI":"10.1093\/nar\/gky1029","article-title":"Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles","volume":"47","author":"Pathan","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507395459800_B21","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.cell.2019.02.018","article-title":"exRNA atlas analysis reveals distinct extracellular RNA cargo types and their carriers present across human biofluids","volume":"177","author":"Murillo","year":"2019","journal-title":"Cell"},{"key":"2022010507395459800_B22","doi-asserted-by":"crossref","first-page":"D106","DOI":"10.1093\/nar\/gkx891","article-title":"exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507395459800_B23","doi-asserted-by":"crossref","first-page":"bbaa088","DOI":"10.1093\/bib\/bbaa088","article-title":"ExoBCD: a comprehensive database for exosomal biomarker discovery in breast cancer","volume":"22","author":"Wang","year":"2021","journal-title":"Brief. Bioinformatics"},{"key":"2022010507395459800_B24","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2022010507395459800_B25","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2022010507395459800_B26","doi-asserted-by":"crossref","first-page":"D155","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: from microRNA sequences to function","volume":"47","author":"Kozomara","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507395459800_B27","doi-asserted-by":"crossref","first-page":"D220","DOI":"10.1093\/nar\/gkz884","article-title":"snoDB: an interactive database of human snoRNA sequences, abundance and interactions","volume":"48","author":"Bouchard-Bourelle","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507395459800_B28","doi-asserted-by":"crossref","first-page":"D184","DOI":"10.1093\/nar\/gkv1309","article-title":"GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes","volume":"44","author":"Chan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507395459800_B29","doi-asserted-by":"crossref","first-page":"D1250","DOI":"10.1093\/nar\/gky1206","article-title":"RNAcentral: a hub of information for non-coding RNA sequences","volume":"47","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507395459800_B30","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1093\/bib\/bbx074","article-title":"SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data","volume":"19","author":"Zhang","year":"2018","journal-title":"Brief. Bioinformatics"},{"key":"2022010507395459800_B31","doi-asserted-by":"crossref","first-page":"2605","DOI":"10.1093\/bioinformatics\/btz929","article-title":"FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human","volume":"36","author":"Xie","year":"2020","journal-title":"Bioinformatics"},{"key":"2022010507395459800_B32","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1093\/bioinformatics\/bts698","article-title":"SM2miR: a database of the experimentally validated small molecules\u2019 effects on microRNA expression","volume":"29","author":"Liu","year":"2013","journal-title":"Bioinformatics"},{"key":"2022010507395459800_B33","doi-asserted-by":"crossref","first-page":"3771","DOI":"10.1093\/bioinformatics\/bty411","article-title":"GSCALite: a web server for gene set cancer analysis","volume":"34","author":"Liu","year":"2018","journal-title":"Bioinformatics"},{"key":"2022010507395459800_B34","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1002\/2211-5463.12753","article-title":"A panel of miRNAs derived from plasma extracellular vesicles as novel diagnostic biomarkers of lung adenocarcinoma","volume":"9","author":"Yao","year":"2019","journal-title":"FEBS Open Bio."},{"key":"2022010507395459800_B35","doi-asserted-by":"crossref","first-page":"83913","DOI":"10.18632\/oncotarget.19996","article-title":"Selective secretion of microRNAs from lung cancer cells via extracellular vesicles promotes CAMK1D-mediated tube formation in endothelial cells","volume":"8","author":"Lawson","year":"2017","journal-title":"Oncotarget"},{"key":"2022010507395459800_B36","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s13578-018-0202-x","article-title":"Characterization and selective incorporation of small non-coding RNAs in non-small cell lung cancer extracellular vesicles","volume":"8","author":"Li","year":"2018","journal-title":"Cell Biosci."},{"key":"2022010507395459800_B37","first-page":"5554","article-title":"MiR-451a suppressed cell migration and invasion in non-small cell lung cancer through targeting ATF2","volume":"22","author":"Shen","year":"2018","journal-title":"Eur. Rev. Med. Pharmacol Sci."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D111\/42058402\/gkab668.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D111\/42058402\/gkab668.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T08:17:22Z","timestamp":1641370642000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D111\/6350764"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,13]]},"references-count":37,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,8,13]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab668","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,8,13]]}}}