{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T04:48:41Z","timestamp":1773809321023,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1597,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Although small non-coding RNAs, such as microRNAs, have well-established functions in the cell, long non-coding RNAs (lncRNAs) have only recently started to emerge as abundant regulators of cell physiology, and their functions may be diverse. A small number of studies describe interactions between small and lncRNAs, with lncRNAs acting either as inhibitory decoys or as regulatory targets of microRNAs, but such interactions are still poorly explored. To facilitate the study of microRNA\u2013lncRNA interactions, we implemented miRcode: a comprehensive searchable map of putative microRNA target sites across the complete GENCODE annotated transcriptome, including 10 419 lncRNA genes in the current version.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.mircode.org<\/jats:p>\n               <jats:p>Contact: \u00a0erik.larsson@gu.se<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts344","type":"journal-article","created":{"date-parts":[[2012,6,23]],"date-time":"2012-06-23T08:09:48Z","timestamp":1340438988000},"page":"2062-2063","source":"Crossref","is-referenced-by-count":592,"title":["miRcode: a map of putative microRNA target sites in the long non-coding transcriptome"],"prefix":"10.1093","volume":"28","author":[{"given":"Ashwini","family":"Jeggari","sequence":"first","affiliation":[{"name":"1 Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden and 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA"}]},{"given":"Debora S","family":"Marks","sequence":"additional","affiliation":[{"name":"1 Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden and 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA"}]},{"given":"Erik","family":"Larsson","sequence":"additional","affiliation":[{"name":"1 Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden and 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,5,19]]},"reference":[{"key":"2023012512452865000_B1","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/msb.2010.24","article-title":"Target mRNA abundance dilutes microRNA and siRNA activity","volume":"6","author":"Arvey","year":"2010","journal-title":"Mol. Syst. Biol."},{"key":"2023012512452865000_B2","doi-asserted-by":"crossref","first-page":"3082","DOI":"10.1038\/emboj.2010.199","article-title":"A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression","volume":"29","author":"Bernard","year":"2010","journal-title":"EMBO J."},{"key":"2023012512452865000_B3","doi-asserted-by":"crossref","first-page":"D149","DOI":"10.1093\/nar\/gkm995","article-title":"The microRNA.org resource: targets and expression","volume":"36","author":"Betel","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512452865000_B4","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"2023012512452865000_B5","doi-asserted-by":"crossref","first-page":"4750","DOI":"10.1038\/onc.2011.193","article-title":"microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer","volume":"30","author":"Braconi","year":"2011","journal-title":"Oncogene"},{"key":"2023012512452865000_B6","first-page":"28","article-title":"The product of the H19 gene may function as an RNA","volume":"10","author":"Brannan","year":"1990","journal-title":"Mol. Cell. Biol."},{"key":"2023012512452865000_B7","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/349038a0","article-title":"A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome","volume":"349","author":"Brown","year":"1991","journal-title":"Nature"},{"key":"2023012512452865000_B8","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.ccr.2007.07.027","article-title":"Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas","volume":"12","author":"Calin","year":"2007","journal-title":"Cancer Cell"},{"key":"2023012512452865000_B9","doi-asserted-by":"crossref","first-page":"1563","DOI":"10.1126\/science.1187197","article-title":"Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA","volume":"328","author":"Cazalla","year":"2010","journal-title":"Science"},{"key":"2023012512452865000_B10","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.cell.2011.09.028","article-title":"A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA","volume":"147","author":"Cesana","year":"2011","journal-title":"Cell"},{"key":"2023012512452865000_B11","doi-asserted-by":"crossref","first-page":"R858","DOI":"10.1016\/j.cub.2010.08.052","article-title":"Emerging roles for natural microRNA sponges","volume":"20","author":"Ebert","year":"2010","journal-title":"Curr. Biol."},{"key":"2023012512452865000_B12","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/ng2079","article-title":"Target mimicry provides a new mechanism for regulation of microRNA activity","volume":"39","author":"Franco-Zorrilla","year":"2007","journal-title":"Nat. Genet."},{"key":"2023012512452865000_B13","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1101\/gr.082701.108","article-title":"Most mammalian mRNAs are conserved targets of microRNAs","volume":"19","author":"Friedman","year":"2009","journal-title":"Genome Res."},{"key":"2023012512452865000_B14","doi-asserted-by":"crossref","first-page":"D876","DOI":"10.1093\/nar\/gkq963","article-title":"The UCSC Genome Browser database: update 2011","volume":"39","author":"Fujita","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512452865000_B15","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.molcel.2007.06.017","article-title":"MicroRNA targeting specificity in mammals: determinants beyond seed pairing","volume":"27","author":"Grimson","year":"2007","journal-title":"Mol. Cell."},{"key":"2023012512452865000_B16","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/nature10398","article-title":"lincRNAs act in the circuitry controlling pluripotency and differentiation","volume":"477","author":"Guttman","year":"2011","journal-title":"Nature"},{"key":"2023012512452865000_B17","doi-asserted-by":"crossref","first-page":"4414","DOI":"10.1038\/emboj.2011.359","article-title":"miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA","volume":"30","author":"Hansen","year":"2011","journal-title":"EMBO J."},{"issue":"Suppl 1","key":"2023012512452865000_B18","doi-asserted-by":"crossref","first-page":"S4.1","DOI":"10.1186\/gb-2006-7-s1-s4","article-title":"GENCODE: producing a reference annotation for ENCODE","volume":"7","author":"Harrow","year":"2006","journal-title":"Genome Biol."},{"key":"2023012512452865000_B19","doi-asserted-by":"crossref","first-page":"ra8","DOI":"10.1126\/scisignal.2000568","article-title":"Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor","volume":"3","author":"Kino","year":"2010","journal-title":"Sci. Signal"},{"key":"2023012512452865000_B20","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/ng1536","article-title":"Combinatorial microRNA target predictions","volume":"37","author":"Krek","year":"2005","journal-title":"Nat. Genet."},{"key":"2023012512452865000_B21","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/S0092-8674(03)01018-3","article-title":"Prediction of mammalian microRNA targets","volume":"115","author":"Lewis","year":"2003","journal-title":"Cell"},{"key":"2023012512452865000_B22","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nrg2521","article-title":"Long non-coding RNAs: insights into functions","volume":"10","author":"Mercer","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2023012512452865000_B23","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nature09144","article-title":"A coding-independent function of gene and pseudogene mRNAs regulates tumour biology","volume":"465","author":"Poliseno","year":"2010","journal-title":"Nature"},{"key":"2023012512452865000_B24","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1016\/j.cell.2007.05.022","article-title":"Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs","volume":"129","author":"Rinn","year":"2007","journal-title":"Cell"},{"key":"2023012512452865000_B25","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature07228","article-title":"Widespread changes in protein synthesis induced by microRNAs","volume":"455","author":"Selbach","year":"2008","journal-title":"Nature"},{"key":"2023012512452865000_B26","doi-asserted-by":"crossref","first-page":"5366","DOI":"10.1093\/nar\/gkq285","article-title":"CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512452865000_B27","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/nature09819","article-title":"A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression","volume":"472","author":"Wang","year":"2011","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/15\/2062\/48873446\/bioinformatics_28_15_2062.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/15\/2062\/48873446\/bioinformatics_28_15_2062.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:21:38Z","timestamp":1674667298000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/15\/2062\/238391"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,5,19]]},"references-count":27,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2012,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts344","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,8,1]]},"published":{"date-parts":[[2012,5,19]]}}}