{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T20:45:59Z","timestamp":1768596359267,"version":"3.49.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,9,6]],"date-time":"2016-09-06T00:00:00Z","timestamp":1473120000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["31520103905"],"award-info":[{"award-number":["31520103905"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National High Technology Research and Development Program (\u2018863\u2019 Program) of China","award":["2014AA021502"],"award-info":[{"award-number":["2014AA021502"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Long non-coding RNAs (lncRNAs) are essential in many molecular pathways, and are frequently associated with disease but the mechanisms of most lncRNAs have not yet been characterized. Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including lncRNA gene regions. As the number of studies on lncRNAs grows rapidly, it is necessary to evaluate the effects of genetic variations on lncRNAs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present LncVar, a database of genetic variation associated with long non-coding genes in six species. We collected lncRNAs from the NONCODE database, and evaluated their conservation. We systematically integrated transcription factor binding sites and m6A modification sites of lncRNAs and provided comprehensive effects of SNPs on transcription and modification of lncRNAs. We collected putatively translated open reading frames (ORFs) in lncRNAs, and identified both synonymous and non-synonymous SNPs in ORFs. We also collected expression quantitative trait loci of lncRNAs from the literature. Furthermore, we identified lncRNAs in CNV regions as prognostic biomarker candidates of cancers and predicted lncRNA gene fusion events from RNA-seq data from cell lines. The LncVar database can be used as a resource to evaluate the effects of the variations on the biological function of lncRNAs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>LncVar is available at http:\/\/bioinfo.ibp.ac.cn\/LncVar.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary materials are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw581","type":"journal-article","created":{"date-parts":[[2016,9,8]],"date-time":"2016-09-08T00:39:31Z","timestamp":1473295171000},"page":"112-118","source":"Crossref","is-referenced-by-count":36,"title":["LncVar: a database of genetic variation associated with long non-coding genes"],"prefix":"10.1093","volume":"33","author":[{"given":"Xiaowei","family":"Chen","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"},{"name":"Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yajing","family":"Hao","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"},{"name":"University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ya","family":"Cui","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"},{"name":"University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Fan","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"},{"name":"Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shunmin","family":"He","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianjun","family":"Luo","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Runsheng","family":"Chen","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"},{"name":"Research Network of Computational Biology, RNCB, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,9,6]]},"reference":[{"key":"2023020204203714500_btw581-B1","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.cell.2015.01.009","article-title":"A micropeptide encoded by a putative long noncoding RNA regulates muscle performance","volume":"160","author":"Anderson","year":"2015","journal-title":"Cell"},{"key":"2023020204203714500_btw581-B2","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1101\/gr.134767.111","article-title":"Long noncoding RNAs are rarely translated in two human cell lines","volume":"22","author":"Banfai","year":"2012","journal-title":"Genome Res"},{"key":"2023020204203714500_btw581-B3","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1016\/j.stem.2014.09.019","article-title":"m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells","volume":"15","author":"Batista","year":"2014","journal-title":"Cell Stem Cell"},{"key":"2023020204203714500_btw581-B4","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1002\/embj.201488411","article-title":"Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation","volume":"33","author":"Bazzini","year":"2014","journal-title":"EMBO J"},{"key":"2023020204203714500_btw581-B5","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/j.ydbio.2013.04.024","article-title":"The role of SOX10 during enteric nervous system development","volume":"382","author":"Bondurand","year":"2013","journal-title":"Dev. Biol"},{"key":"2023020204203714500_btw581-B6","first-page":"431","article-title":"The statistical significance of nucleotide position-weight matrix matches","volume":"12","author":"Claverie","year":"1996","journal-title":"Comput. Appl. Biosci"},{"key":"2023020204203714500_btw581-B7","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/nrg3454","article-title":"Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data","volume":"14","author":"Dekker","year":"2013","journal-title":"Nat. Rev. Genet"},{"key":"2023020204203714500_btw581-B8","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature11112","article-title":"Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq","volume":"485","author":"Dominissini","year":"2012","journal-title":"Nature"},{"key":"2023020204203714500_btw581-B9","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1016\/j.cell.2013.10.026","article-title":"RNA-methylation-dependent RNA processing controls the speed of the circadian clock","volume":"155","author":"Fustin","year":"2013","journal-title":"Cell"},{"key":"2023020204203714500_btw581-B10","doi-asserted-by":"crossref","first-page":"1922","DOI":"10.1093\/bioinformatics\/btr310","article-title":"FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution","volume":"27","author":"Ge","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020204203714500_btw581-B11","doi-asserted-by":"crossref","first-page":"D181","DOI":"10.1093\/nar\/gku1000","article-title":"lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse","volume":"43","author":"Gong","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204203714500_btw581-B12","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nature07672","article-title":"Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals","volume":"458","author":"Guttman","year":"2009","journal-title":"Nature"},{"key":"2023020204203714500_btw581-B13","doi-asserted-by":"crossref","first-page":"5735","DOI":"10.1093\/nar\/18.19.5735","article-title":"Sequence specificity of the human mRNA N6-adenosine methylase in vitro","volume":"18","author":"Harper","year":"1990","journal-title":"Nucleic Acids Res"},{"key":"2023020204203714500_btw581-B14","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1038\/nn.3449","article-title":"The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry","volume":"16","author":"Hess","year":"2013","journal-title":"Nat. Neurosci"},{"key":"2023020204203714500_btw581-B15","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.ccr.2014.07.009","article-title":"A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer","volume":"26","author":"Hu","year":"2014","journal-title":"Cancer Cell"},{"key":"2023020204203714500_btw581-B16","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"2023020204203714500_btw581-B17","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","article-title":"Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes","volume":"147","author":"Ingolia","year":"2011","journal-title":"Cell"},{"key":"2023020204203714500_btw581-B18","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/ng.3192","article-title":"The landscape of long noncoding RNAs in the human transcriptome","volume":"47","author":"Iyer","year":"2015","journal-title":"Nat. Genet"},{"key":"2023020204203714500_btw581-B19","doi-asserted-by":"crossref","first-page":"8646","DOI":"10.1073\/pnas.1205654109","article-title":"The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type","volume":"109","author":"Jendrzejewski","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020204203714500_btw581-B20","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nature12644","article-title":"A high-resolution map of the three-dimensional chromatin interactome in human cells","volume":"503","author":"Jin","year":"2013","journal-title":"Nature"},{"key":"2023020204203714500_btw581-B21","doi-asserted-by":"crossref","first-page":"e1003201.","DOI":"10.1371\/journal.pgen.1003201","article-title":"Human disease-associated genetic variation impacts large intergenic non-coding RNA expression","volume":"9","author":"Kumar","year":"2013","journal-title":"PLoS Genet"},{"key":"2023020204203714500_btw581-B22","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1146\/annurev-genom-090413-025405","article-title":"The pivotal regulatory landscape of RNA modifications","volume":"15","author":"Li","year":"2014","journal-title":"Annu. Rev. Genomics Hum. Genet"},{"key":"2023020204203714500_btw581-B23","doi-asserted-by":"crossref","first-page":"5630.","DOI":"10.1038\/ncomms6630","article-title":"Unique features of the m6A methylome in Arabidopsis thaliana","volume":"5","author":"Luo","year":"2014","journal-title":"Nat. Commun"},{"key":"2023020204203714500_btw581-B24","doi-asserted-by":"crossref","first-page":"e11824.","DOI":"10.1371\/journal.pone.0011824","article-title":"Genome-wide association study of pancreatic cancer in Japanese population","volume":"5","author":"Low","year":"2010","journal-title":"PLoS One"},{"key":"2023020204203714500_btw581-B25","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nmeth.3205","article-title":"Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes","volume":"12","author":"Ma","year":"2015","journal-title":"Nat. Methods"},{"key":"2023020204203714500_btw581-B26","doi-asserted-by":"crossref","first-page":"D110","DOI":"10.1093\/nar\/gkv1176","article-title":"JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles","volume":"44","author":"Mathelier","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020204203714500_btw581-B27","doi-asserted-by":"crossref","first-page":"e1001138.","DOI":"10.1371\/journal.pcbi.1001138","article-title":"deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data","volume":"7","author":"McPherson","year":"2011","journal-title":"PLoS Comput. Biol"},{"key":"2023020204203714500_btw581-B28","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","article-title":"Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"key":"2023020204203714500_btw581-B29","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nature08903","article-title":"Transcriptome genetics using second generation sequencing in a Caucasian population","volume":"464","author":"Montgomery","year":"2010","journal-title":"Nature"},{"key":"2023020204203714500_btw581-B30","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.cancergencyto.2008.01.013","article-title":"The GAS5 (growth arrest-specific transcript 5) gene fuses to BCL6 as a result of t(1;3)(q25;q27) in a patient with B-cell lymphoma","volume":"182","author":"Nakamura","year":"2008","journal-title":"Cancer Genet. Cytogenet"},{"key":"2023020204203714500_btw581-B31","doi-asserted-by":"crossref","first-page":"152.","DOI":"10.1186\/1471-2105-15-152","article-title":"LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs","volume":"15","author":"Ning","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020204203714500_btw581-B32","doi-asserted-by":"crossref","first-page":"e81925.","DOI":"10.1371\/journal.pone.0081925","article-title":"Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors","volume":"8","author":"Norton","year":"2013","journal-title":"PLoS One"},{"key":"2023020204203714500_btw581-B33","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1016\/j.ccell.2014.09.014","article-title":"The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation","volume":"26","author":"Pandey","year":"2014","journal-title":"Cancer Cell"},{"key":"2023020204203714500_btw581-B34","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020204203714500_btw581-B35","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1126\/science.aaf4405","article-title":"Hypoxic control of metastasis","volume":"352","author":"Rankin","year":"2016","journal-title":"Science"},{"key":"2023020204203714500_btw581-B36","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/cr.2012.30","article-title":"RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings","volume":"22","author":"Ren","year":"2012","journal-title":"Cell Res"},{"key":"2023020204203714500_btw581-B37","doi-asserted-by":"crossref","first-page":"D670","DOI":"10.1093\/nar\/gku1177","article-title":"The UCSC Genome Browser database: 2015 update","volume":"43","author":"Rosenbloom","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020204203714500_btw581-B38","doi-asserted-by":"crossref","first-page":"e03523.","DOI":"10.7554\/eLife.03523","article-title":"Long non-coding RNAs as a source of new peptides","volume":"3","author":"Ruiz-Orera","year":"2014","journal-title":"Elife"},{"key":"2023020204203714500_btw581-B39","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nature11279","article-title":"The long-range interaction landscape of gene promoters","volume":"489","author":"Sanyal","year":"2012","journal-title":"Nature"},{"key":"2023020204203714500_btw581-B40","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes","volume":"15","author":"Siepel","year":"2005","journal-title":"Genome Res"},{"key":"2023020204203714500_btw581-B41","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nchembio.1120","article-title":"Peptidomic discovery of short open reading frame-encoded peptides in human cells","volume":"9","author":"Slavoff","year":"2013","journal-title":"Nat. Chem. Biol"},{"key":"2023020204203714500_btw581-B42","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020204203714500_btw581-B43","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.cell.2013.06.020","article-title":"lincRNAs: genomics, evolution, and mechanisms","volume":"154","author":"Ulitsky","year":"2013","journal-title":"Cell"},{"key":"2023020204203714500_btw581-B44","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nature12730","article-title":"N6-methyladenosine-dependent regulation of messenger RNA stability","volume":"505","author":"Wang","year":"2014","journal-title":"Nature"},{"key":"2023020204203714500_btw581-B45","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/ncb2902","article-title":"N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells","volume":"16","author":"Wang","year":"2014","journal-title":"Nat. Cell Biol"},{"key":"2023020204203714500_btw581-B46","doi-asserted-by":"crossref","first-page":"1672","DOI":"10.1021\/bi00627a023","article-title":"Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid","volume":"16","author":"Wei","year":"1977","journal-title":"Biochemistry"},{"key":"2023020204203714500_btw581-B47","doi-asserted-by":"crossref","first-page":"D1001","DOI":"10.1093\/nar\/gkt1229","article-title":"The NHGRI GWAS Catalog, a curated resource of SNP-trait associations","volume":"42","author":"Welter","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204203714500_btw581-B48","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/nature13319","article-title":"Mass-spectrometry-based draft of the human proteome","volume":"509","author":"Wilhelm","year":"2014","journal-title":"Nature"},{"key":"2023020204203714500_btw581-B49","doi-asserted-by":"crossref","first-page":"D98","DOI":"10.1093\/nar\/gkt1222","article-title":"NONCODEv4: exploring the world of long non-coding RNA genes","volume":"42","author":"Xie","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204203714500_btw581-B50","doi-asserted-by":"crossref","first-page":"1778 e1779","DOI":"10.1016\/j.neurobiolaging.2014.01.014","article-title":"Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations","volume":"35","author":"Xie","year":"2014","journal-title":"Neurobiol. Aging"},{"key":"2023020204203714500_btw581-B51","doi-asserted-by":"crossref","first-page":"R137.","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol"},{"key":"2023020204203714500_btw581-B52","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/cr.2014.151","article-title":"FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis","volume":"24","author":"Zhao","year":"2014","journal-title":"Cell Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/1\/112\/49037408\/bioinformatics_33_1_112.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/1\/112\/49037408\/bioinformatics_33_1_112.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:21:42Z","timestamp":1675311702000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/1\/112\/2525690"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,9,6]]},"references-count":52,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw581","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,1,1]]},"published":{"date-parts":[[2016,9,6]]}}}