{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T20:30:37Z","timestamp":1780518637124,"version":"3.54.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,4,25]],"date-time":"2023-04-25T00:00:00Z","timestamp":1682380800000},"content-version":"vor","delay-in-days":114,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["R01DK124228 R01DK124228-02S1"],"award-info":[{"award-number":["R01DK124228 R01DK124228-02S1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>MicroRNAs (miRs) may contribute to disease etiology by influencing gene expression. Numerous databases are available for miR target prediction and validation, but their functionality is varied, and outputs are not standardized. The purpose of this review is to identify and describe databases for cataloging validated miR targets. Using Tools4miRs and PubMed, we identified databases with experimentally validated targets, human data, and a focus on miR\u2013messenger RNA (mRNA) interactions. Data were extracted about the number of times each database was cited, the number of miRs, the target genes, the interactions per database, experimental methodology and key features of each database. The search yielded 10 databases, which in order of most cited to least were: miRTarBase, starBase\/The Encyclopedia of RNA Interactomes, DIANA-TarBase, miRWalk, miRecords, miRGator, miRSystem, miRGate, miRSel and targetHub. Findings from this review suggest that the information presented within miR target validation databases can be enhanced by adding features such as flexibility in performing queries in multiple ways, downloadable data, ongoing updates and integrating tools for further miR\u2013mRNA target interaction analysis. This review is designed to aid researchers, especially those new to miR bioinformatics tools, in database selection and to offer considerations for future development and upkeep of validation tools.<\/jats:p>\n               <jats:p>Database URL http:\/\/mirtarbase.cuhk.edu.cn\/<\/jats:p>","DOI":"10.1093\/database\/baad014","type":"journal-article","created":{"date-parts":[[2023,4,25]],"date-time":"2023-04-25T22:22:31Z","timestamp":1682461351000},"source":"Crossref","is-referenced-by-count":37,"title":["Review of databases for experimentally validated human microRNA\u2013mRNA interactions"],"prefix":"10.1093","volume":"2023","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8607-6185","authenticated-orcid":false,"given":"Dorian","family":"Kariuki","sequence":"first","affiliation":[{"name":"Department of Physiological Nursing, University of California , San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kesava","family":"Asam","sequence":"additional","affiliation":[{"name":"Bluestone Center for Clinical Research, New York University , New York, CA 10010, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bradley E","family":"Aouizerat","sequence":"additional","affiliation":[{"name":"Bluestone Center for Clinical Research, New York University , New York, CA 10010, USA"},{"name":"Department of Oral and Maxillofacial Surgery, New York University , New York, CA 10010, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly A","family":"Lewis","sequence":"additional","affiliation":[{"name":"Department of Physiological Nursing, University of California , San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose C","family":"Florez","sequence":"additional","affiliation":[{"name":"Department of Medicine, Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital , Boston, MA 02114, USA"},{"name":"Programs in Metabolism and Medical & Population Genetics, Broad Institute , Cambridge, MA 02142, USA"},{"name":"Department of Medicine, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7054-7533","authenticated-orcid":false,"given":"Elena","family":"Flowers","sequence":"additional","affiliation":[{"name":"Department of Physiological Nursing, University of California , San Francisco, CA 94143, USA"},{"name":"Institute for Human Genetics, University of California , San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,4,25]]},"reference":[{"key":"2023042522222085200_R1","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-021-88617-6","article-title":"The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature","volume":"11","author":"Pirr\u00f2","year":"2021","journal-title":"Sci. Rep."},{"key":"2023042522222085200_R2","doi-asserted-by":"crossref","first-page":"4","DOI":"10.2174\/2211536607666180827111633","article-title":"MiRNAs: biology, biogenesis, their web-based tools, and databases","volume":"8","author":"Tafrihi","year":"2019","journal-title":"Microrna"},{"key":"2023042522222085200_R3","doi-asserted-by":"crossref","first-page":"D155","DOI":"10.1093\/nar\/gkn809","article-title":"The database of experimentally supported targets: a functional update of TarBase","volume":"37","author":"Papadopoulos","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R4","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2021.104544","article-title":"An updated overview and classification of bioinformatics tools for microRNA analysis, which one to choose?","volume":"134","author":"Mortazavi","year":"2021","journal-title":"Comput. Biol. Med."},{"key":"2023042522222085200_R5","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.1002\/jcp.25854","article-title":"Interplay between miRNAs and human diseases","volume":"233","author":"Paul","year":"2018","journal-title":"J. Cell. Physiol."},{"key":"2023042522222085200_R6","doi-asserted-by":"crossref","first-page":"1836","DOI":"10.1093\/bib\/bby054","article-title":"Trends in the development of miRNA bioinformatics tools","volume":"20","author":"Chen","year":"2019","journal-title":"Brief. Bioinformatics"},{"key":"2023042522222085200_R7","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/978-1-62703-748-8_12","volume-title":"miRNomics: MicroRNA Biology and Computational Analysis","author":"Hamzeiy","year":"2014"},{"key":"2023042522222085200_R8","doi-asserted-by":"crossref","DOI":"10.3390\/mps4010001","article-title":"miRNA targets: from prediction tools to experimental validation","volume":"4","author":"Riolo","year":"2020","journal-title":"Methods Protoc."},{"key":"2023042522222085200_R9","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.ygeno.2012.08.006","article-title":"miRNA Targets: a database for miRNA target predictions in coding and non-coding regions of mRNAs","volume":"100","author":"Kumar","year":"2012","journal-title":"Genomics"},{"key":"2023042522222085200_R10","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkab1079","article-title":"miRTarBase update 2022: an informative resource for experimentally validated miRNA\u2013target interactions","volume":"50","author":"Huang","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R11","doi-asserted-by":"crossref","first-page":"D202","DOI":"10.1093\/nar\/gkq1056","article-title":"starBase: a database for exploring microRNA\u2013mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data","volume":"39","author":"Yang","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R12","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/978-1-4939-8982-9_9","volume-title":"Computational Biology of Non-Coding RNA","author":"Monga","year":"2019"},{"key":"2023042522222085200_R13","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1002\/ddr.21278","article-title":"Validated microRNA target databases: an evaluation","volume":"76","author":"Ji Diana Lee","year":"2015","journal-title":"Drug Dev. Res."},{"key":"2023042522222085200_R14","doi-asserted-by":"crossref","first-page":"2722","DOI":"10.1093\/bioinformatics\/btw189","article-title":"Tools4miRs - one place to gather all the tools for miRNA analysis","volume":"32","author":"Lukasik","year":"2016","journal-title":"Bioinformatics"},{"key":"2023042522222085200_R15","article-title":"The PRISMA 2020 statement: an updated guideline for reporting systematic reviews","volume":"372","author":"Page","year":"2021","journal-title":"Bmj"},{"key":"2023042522222085200_R16","doi-asserted-by":"crossref","first-page":"D239","DOI":"10.1093\/nar\/gkv1258","article-title":"miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database","volume":"44","author":"Chou","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R17","doi-asserted-by":"crossref","first-page":"D296","DOI":"10.1093\/nar\/gkx1067","article-title":"miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions","volume":"46","author":"Chou","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R18","doi-asserted-by":"crossref","first-page":"D163","DOI":"10.1093\/nar\/gkq1107","article-title":"miRTarBase: a database curates experimentally validated microRNA\u2013target interactions","volume":"39","author":"Hsu","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R19","doi-asserted-by":"crossref","first-page":"D78","DOI":"10.1093\/nar\/gkt1266","article-title":"miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions","volume":"42","author":"Hsu","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R20","first-page":"D148","article-title":"miRTarBase 2020: updates to the experimentally validated microRNA\u2013target interaction database","volume":"48","author":"Huang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R21","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","article-title":"starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein\u2013RNA interaction networks from large-scale CLIP-Seq data","volume":"42","author":"Li","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R22","doi-asserted-by":"crossref","first-page":"D239","DOI":"10.1093\/nar\/gkx1141","article-title":"DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions","volume":"46","author":"Karagkouni","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R23","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1261\/rna.2239606","article-title":"TarBase: A comprehensive database of experimentally supported animal microRNA targets","volume":"12","author":"Sethupathy","year":"2006","journal-title":"RNA"},{"key":"2023042522222085200_R24","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkr1161","article-title":"TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support","volume":"40","author":"Vergoulis","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R25","doi-asserted-by":"crossref","first-page":"D153","DOI":"10.1093\/nar\/gku1215","article-title":"DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions","volume":"43","author":"Vlachos","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023042522222085200_R26","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1016\/j.jbi.2011.05.002","article-title":"miRWalk\u2014database: prediction of possible miRNA binding sites by \u201cwalking\u201d the genes of three genomes","volume":"44","author":"Dweep","year":"2011","journal-title":"J. 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Biol."},{"key":"2023042522222085200_R35","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bav035","article-title":"miRGate: a curated database of human, mouse and rat miRNA-mRNA targets","volume":"2015","author":"Andr\u00e9s-Le\u00f3n","year":"2015","journal-title":"Database (Oxford)"},{"key":"2023042522222085200_R36","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-11-135","article-title":"miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature","volume":"11","author":"Naeem","year":"2010","journal-title":"BMC Bioinform."},{"key":"2023042522222085200_R37","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1093\/bioinformatics\/btt439","article-title":"targetHub: a programmable interface for miRNA-gene interactions","volume":"29","author":"Manyam","year":"2013","journal-title":"Bioinformatics"},{"key":"2023042522222085200_R38","article-title":"ENCORI: The Encyclopedia of RNA Interactomes","author":"Zhou"},{"key":"2023042522222085200_R39","doi-asserted-by":"crossref","DOI":"10.3892\/mmr.2022.12672","article-title":"Coexpressed microRNAs, target genes and pathways related to metabolism, inflammation and endocrine function in individuals at risk for type 2 diabetes","volume":"25","author":"Flowers","year":"2022","journal-title":"Mol. 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Metab."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad014\/50097252\/baad014.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad014\/50097252\/baad014.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,25]],"date-time":"2023-04-25T22:22:59Z","timestamp":1682461379000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baad014\/7142843"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,1]]},"references-count":40,"URL":"https:\/\/doi.org\/10.1093\/database\/baad014","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2023,1,1]]},"article-number":"baad014"}}