{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T05:33:36Z","timestamp":1780724016916,"version":"3.54.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,9,12]],"date-time":"2019-09-12T00:00:00Z","timestamp":1568246400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970644"],"award-info":[{"award-number":["31970644"]}],"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":["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":["31771458"],"award-info":[{"award-number":["31771458"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Huazhong Agricultural University Scientific\u00a0& Technological Self-innovation Foundation","award":["11041810351"],"award-info":[{"award-number":["11041810351"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Alternative polyadenylation (APA) is an important post-transcriptional regulation that recognizes different polyadenylation signals (PASs), resulting in transcripts with different 3\u2032 untranslated regions, thereby influencing a series of biological processes and functions. Recent studies have revealed that some single nucleotide polymorphisms (SNPs) could contribute to tumorigenesis and development through dysregulating APA. However, the associations between SNPs and APA in human cancers remain largely unknown. Here, using genotype and APA data of 9082 samples from The Cancer Genome Atlas (TCGA) and The Cancer 3\u2032UTR Altas (TC3A), we systematically identified SNPs affecting APA events across 32 cancer types and defined them as APA quantitative trait loci (apaQTLs). As a result, a total of 467 942 cis-apaQTLs and 30 721 trans-apaQTLs were identified. By integrating apaQTLs with survival and genome-wide association studies (GWAS) data, we further identified 2154 apaQTLs associated with patient survival time and 151\u00a0342 apaQTLs located in GWAS loci. In addition, we designed an online tool to predict the effects of SNPs on PASs by utilizing PAS motif prediction tool. Finally, we developed SNP2APA, a user-friendly and intuitive database (http:\/\/gong_lab.hzau.edu.cn\/SNP2APA\/) for data browsing, searching, and downloading. SNP2APA will significantly improve our understanding of genetic variants and APA in human cancers.<\/jats:p>","DOI":"10.1093\/nar\/gkz793","type":"journal-article","created":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T19:32:29Z","timestamp":1567798349000},"page":"D226-D232","source":"Crossref","is-referenced-by-count":47,"title":["SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers"],"prefix":"10.1093","volume":"48","author":[{"given":"Yanbo","family":"Yang","sequence":"first","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Hubei Bioinformatics and 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 430074, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Ru","family":"Miao","sequence":"additional","affiliation":[{"name":"Hubei Bioinformatics and 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 430074, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajun","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqian","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangda","family":"Yu","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Hubei Bioinformatics and 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 430074, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Gong","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China"},{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,9,12]]},"reference":[{"key":"2020010521380052600_B1","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1101\/gr.202432.115","article-title":"A comprehensive analysis of 3\u2032 end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation","volume":"26","author":"Gruber","year":"2016","journal-title":"Genome Res."},{"key":"2020010521380052600_B2","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/nrm.2016.116","article-title":"Alternative polyadenylation of mRNA precursors","volume":"18","author":"Tian","year":"2017","journal-title":"Nat. Rev. Mol. 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Histochem. Cytochem."},{"key":"2020010521380052600_B36","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btr602","article-title":"Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences","volume":"28","author":"Kalkatawi","year":"2012","journal-title":"Bioinformatics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D226\/31697189\/gkz793.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D226\/31697189\/gkz793.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T23:34:52Z","timestamp":1611012892000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D226\/5568208"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,12]]},"references-count":36,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2019,9,12]]},"published-print":{"date-parts":[[2020,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz793","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1,8]]},"published":{"date-parts":[[2019,9,12]]}}}