{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T07:45:45Z","timestamp":1780386345776,"version":"3.54.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"S19","license":[{"start":{"date-parts":[[2018,12,1]],"date-time":"2018-12-01T00:00:00Z","timestamp":1543622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2531-5","type":"journal-article","created":{"date-parts":[[2018,12,31]],"date-time":"2018-12-31T03:43:12Z","timestamp":1546227792000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["miRBaseConverter: an R\/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase"],"prefix":"10.1186","volume":"19","author":[{"given":"Taosheng","family":"Xu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junpeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongqiang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weijia","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Gui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kui","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiuyong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thuc Duy","family":"Le","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,12,31]]},"reference":[{"key":"2531_CR1","doi-asserted-by":"crossref","unstructured":"Ambros V. The functions of animal microRNAs. Nature. 2004; 431(7006):350\u20135. https:\/\/doi.org\/10.1038\/nature02871 .","DOI":"10.1038\/nature02871"},{"key":"2531_CR2","doi-asserted-by":"crossref","unstructured":"Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116(2):281\u201397. https:\/\/doi.org\/doi:10.1016\/S0092-8674(04)00045-5 .","DOI":"10.1016\/S0092-8674(04)00045-5"},{"issue":"7308","key":"2531_CR3","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1038\/nature09267","volume":"466","author":"H Guo","year":"2010","unstructured":"Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian micrornas predominantly act to decrease target mrna levels. Nature. 2010; 466(7308):835.","journal-title":"Nature"},{"issue":"2","key":"2531_CR4","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nrg2936","volume":"12","author":"E Huntzinger","year":"2011","unstructured":"Huntzinger E, Izaurralde E. Gene silencing by micrornas: contributions of translational repression and mrna decay. Nat Rev Genet. 2011; 12(2):99.","journal-title":"Nat Rev Genet"},{"issue":"11","key":"2531_CR5","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1038\/nrc1997","volume":"6","author":"GA Calin","year":"2006","unstructured":"Calin GA, Croce CM. Microrna signatures in human cancers. Nat Rev Cancer. 2006; 6(11):857.","journal-title":"Nat Rev Cancer"},{"issue":"6","key":"2531_CR6","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1038\/nrc3932","volume":"15","author":"S Lin","year":"2015","unstructured":"Lin S, Gregory RI. Microrna biogenesis pathways in cancer. Nat Rev Cancer. 2015; 15(6):321.","journal-title":"Nat Rev Cancer"},{"issue":"5","key":"2531_CR7","doi-asserted-by":"publisher","first-page":"1004","DOI":"10.1038\/leu.2014.351","volume":"29","author":"K Musilova","year":"2015","unstructured":"Musilova K, Mraz M. Micrornas in b-cell lymphomas: how a complex biology gets more complex. Leukemia. 2015; 29(5):1004.","journal-title":"Leukemia"},{"key":"2531_CR8","doi-asserted-by":"crossref","unstructured":"Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, et al. A uniform system for microrna annotation. RNA. 2003; 9(3):277\u20139. https:\/\/doi.org\/10.1261\/rna.2183803 .","DOI":"10.1261\/rna.2183803"},{"key":"2531_CR9","doi-asserted-by":"crossref","unstructured":"Griffiths-Jones S. The microRNA registry. Nucleic Acids Res. 2004; 32(suppl_1):109\u201311. https:\/\/doi.org\/doi:10.1093\/nar\/gkh023 .","DOI":"10.1093\/nar\/gkh023"},{"key":"2531_CR10","doi-asserted-by":"crossref","unstructured":"Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011; 39(Database issue):152\u20137. https:\/\/doi.org\/doi:10.1093\/nar\/gkq1027 .","DOI":"10.1093\/nar\/gkq1027"},{"issue":"6","key":"2531_CR11","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1261\/rna.965408","volume":"14","author":"X Wang","year":"2008","unstructured":"Wang X. mirdb: a microrna target prediction and functional annotation database with a wiki interface. Rna. 2008; 14(6):1012\u20137.","journal-title":"Rna"},{"issue":"D1","key":"2531_CR12","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1093\/nar\/gkt1248","volume":"42","author":"J-H Li","year":"2013","unstructured":"Li J-H, Liu S, Zhou H, Qu L-H, Yang J-H. starbase v2. 0: decoding mirna-cerna, mirna-ncrna and protein\u2013rna interaction networks from large-scale clip-seq data. Nucleic Acids Res. 2013; 42(D1):92\u20137.","journal-title":"Nucleic Acids Res"},{"key":"2531_CR13","doi-asserted-by":"publisher","first-page":"e05005","DOI":"10.7554\/eLife.05005","volume":"4","author":"V Agarwal","year":"2015","unstructured":"Agarwal V, Bell GW, Nam J-W, Bartel DP. Predicting effective microrna target sites in mammalian mrnas. Elife. 2015; 4:e05005.","journal-title":"Elife"},{"issue":"suppl_1","key":"2531_CR14","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1093\/nar\/gkj112","volume":"34","author":"S Griffiths-Jones","year":"2006","unstructured":"Griffiths-Jones S, Grocock RJ, Van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006; 34(suppl_1):140\u20134.","journal-title":"Nucleic Acids Res"},{"key":"2531_CR15","doi-asserted-by":"crossref","unstructured":"Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008; 36(Database issue):154\u20138. https:\/\/doi.org\/doi:10.1093\/nar\/gkm952 .","DOI":"10.1093\/nar\/gkm952"},{"key":"2531_CR16","doi-asserted-by":"crossref","unstructured":"Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014; 42(D1):68\u201373. https:\/\/doi.org\/doi:10.1093\/nar\/gkt1181 . Accessed 07 July 2017.","DOI":"10.1093\/nar\/gkt1181"},{"issue":"10","key":"2531_CR17","doi-asserted-by":"publisher","first-page":"47786","DOI":"10.1371\/journal.pone.0047786","volume":"7","author":"F Russo","year":"2012","unstructured":"Russo F, Di Bella S, Nigita G, Macca V, Lagana A, Giugno R, Pulvirenti A, Ferro A. miRandola: extracellular circulating microRNAs database. PLoS ONE. 2012; 7(10):47786.","journal-title":"PLoS ONE"},{"issue":"8","key":"2531_CR18","doi-asserted-by":"publisher","first-page":"42390","DOI":"10.1371\/journal.pone.0042390","volume":"7","author":"T-P Lu","year":"2012","unstructured":"Lu T-P, Lee C-Y, Tsai M-H, Chiu Y-C, Hsiao CK, Lai L-C, Chuang EY. miRSystem: an integrated system for characterizing enriched functions and pathways of microrna targets. PLoS ONE. 2012; 7(8):42390.","journal-title":"PLoS ONE"},{"issue":"W1","key":"2531_CR19","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1093\/nar\/gkv381","volume":"43","author":"RJ Bonnal","year":"2015","unstructured":"Bonnal RJ, Rossi RL, Carpi D, Ranzani V, Abrignani S, Pagani M. miRiadne: a web tool for consistent integration of miRNA nomenclature. Nucleic Acids Res. 2015; 43(W1):487\u201392.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"2531_CR20","first-page":"0145386","volume":"10","author":"TD Le","year":"2015","unstructured":"Le TD, Zhang J, Liu L, Liu H, Li J. miRLAB: An R based dry lab for exploring miRNA-mRNA regulatory relationships. PLoS ONE. 2015; 10(12):0145386.","journal-title":"PLoS ONE"},{"issue":"4","key":"2531_CR21","first-page":"592","volume":"33","author":"SJ Haunsberger","year":"2016","unstructured":"Haunsberger SJ, Connolly NM, Prehn JH. miRNAmeConverter: an R\/Bioconductor package for translating mature miRNA names to different miRBase versions. Bioinformatics. 2016; 33(4):592\u20133.","journal-title":"Bioinformatics"},{"key":"2531_CR22","doi-asserted-by":"publisher","first-page":"080","DOI":"10.1093\/database\/bau080","volume":"2014","author":"G Van Peer","year":"2014","unstructured":"Van Peer G, Lefever S, Anckaert J, Beckers A, Rihani A, Van Goethem A, Volders P-J, Zeka F, Ongenaert M, Mestdagh P, et al. mirbase tracker: keeping track of microrna annotation changes. Database. 2014; 2014:080.","journal-title":"Database"},{"issue":"W1","key":"2531_CR23","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1093\/nar\/gkw345","volume":"44","author":"C Backes","year":"2016","unstructured":"Backes C, Khaleeq QT, Meese E, Keller A. mieaa: microrna enrichment analysis and annotation. Nucleic Acids Res. 2016; 44(W1):110\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2531_CR24","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1093\/nar\/gku1215","volume":"43","author":"IS Vlachos","year":"2014","unstructured":"Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos I-L, Maniou S, Karathanou K, Kalfakakou D, et al. DIANA-TarBase v7. 0: indexing more than half a million experimentally supported miRNA: mRNA interactions. Nucleic Acids Res. 2014; 43(D1):153\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2531_CR25","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1093\/nar\/gkx1067","volume":"46","author":"C-H Chou","year":"2017","unstructured":"Chou C-H, Shrestha S, Yang C-D, Chang N-W, Lin Y-L, Liao K-W, Huang W-C, Sun T-H, Tu S-J, Lee W-H, et al. mirtarbase update 2018: a resource for experimentally validated microrna-target interactions. Nucleic Acids Res. 2017; 46(D1):296\u2013302.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"2531_CR26","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):80.","journal-title":"Genome Biol"},{"issue":"suppl_1","key":"2531_CR27","first-page":"105","volume":"37","author":"F Xiao","year":"2008","unstructured":"Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microrna\u2013target interactions. Nucleic Acids Res. 2008; 37(suppl_1):105\u201310.","journal-title":"Nucleic Acids Res"},{"issue":"suppl_1","key":"2531_CR28","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1093\/nar\/gkp803","volume":"38","author":"J Wang","year":"2009","unstructured":"Wang J, Lu M, Qiu C, Cui Q. Transmir: a transcription factor\u2013microrna regulation database. Nucleic Acids Res. 2009; 38(suppl_1):119\u201322.","journal-title":"Nucleic Acids Res"},{"issue":"7414","key":"2531_CR29","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1038\/nature11245","volume":"489","author":"MB Gerstein","year":"2012","unstructured":"Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, et al. Architecture of the human regulatory network derived from encode data. Nature. 2012; 489(7414):91.","journal-title":"Nature"},{"issue":"suppl_1","key":"2531_CR30","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1093\/nar\/gkl1041","volume":"35","author":"C Jiang","year":"2007","unstructured":"Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 2007; 35(suppl_1):137\u201340.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"2531_CR31","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498\u2013504.","journal-title":"Genome Res"},{"issue":"5013","key":"2531_CR32","doi-asserted-by":"publisher","first-page":"1708","DOI":"10.1126\/science.2047879","volume":"252","author":"SE Kern","year":"1991","unstructured":"Kern SE, Kinzler KW, Bruskin A, Jarosz D, Friedman P, Prives C, Vogelstein B. Identification of p53 as a sequence-specific dna-binding protein. Science. 1991; 252(5013):1708\u201311.","journal-title":"Science"},{"issue":"3","key":"2531_CR33","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1038\/nrd4236","volume":"13","author":"KH Khoo","year":"2014","unstructured":"Khoo KH, Verma CS, Lane DP. Drugging the p53 pathway: understanding the route to clinical efficacy. Nat Rev Drug Discov. 2014; 13(3):217\u201336.","journal-title":"Nat Rev Drug Discov"},{"issue":"1","key":"2531_CR34","doi-asserted-by":"crossref","first-page":"624","DOI":"10.18632\/oncotarget.13483","volume":"8","author":"X Wang","year":"2017","unstructured":"Wang X, Sun Q. Tp53 mutations, expression and interaction networks in human cancers. Oncotarget. 2017; 8(1):624.","journal-title":"Oncotarget"},{"issue":"1","key":"2531_CR35","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1186\/1471-2105-6-233","volume":"6","author":"JL Morrison","year":"2005","unstructured":"Morrison JL, Breitling R, Higham DJ, Gilbert DR. Generank: using search engine technology for the analysis of microarray experiments. BMC Bioinforma. 2005; 6(1):233.","journal-title":"BMC Bioinforma"},{"issue":"1","key":"2531_CR36","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/1471-2105-15-37","volume":"15","author":"Y Liu","year":"2014","unstructured":"Liu Y, Gu Q, Hou JP, Han J, Ma J. A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. BMC Bioinforma. 2014; 15(1):37.","journal-title":"BMC Bioinforma"},{"issue":"4","key":"2531_CR37","first-page":"0152792","volume":"11","author":"T Xu","year":"2016","unstructured":"Xu T, Le TD, Liu L, Wang R, Sun B, Li J. Identifying cancer subtypes from miRNA-TF-mRNA regulatory networks and expression data. PLoS ONE. 2016; 11(4):0152792.","journal-title":"PLoS ONE"},{"issue":"6","key":"2531_CR38","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1038\/nmeth.2956","volume":"11","author":"Y Zhu","year":"2014","unstructured":"Zhu Y, Qiu P, Ji Y. TCGA-Assembler: open-source software for retrieving and processing tcga data. Nat Methods. 2014; 11(6):599\u2013600.","journal-title":"Nat Methods"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2531-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2531-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2531-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,21]],"date-time":"2020-11-21T00:19:02Z","timestamp":1605917942000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2531-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":38,"journal-issue":{"issue":"S19","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2531"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2531-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/407148","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]},"assertion":[{"value":"31 December 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"514"}}