{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T05:07:50Z","timestamp":1769922470623,"version":"3.49.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,10,5]],"date-time":"2019-10-05T00:00:00Z","timestamp":1570233600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004917","name":"Cancer Prevention & Research Institute of Texas","doi-asserted-by":"publisher","award":["RR150085"],"award-info":[{"award-number":["RR150085"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA175486"],"award-info":[{"award-number":["CA175486"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA209851"],"award-info":[{"award-number":["CA209851"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA016672"],"award-info":[{"award-number":["CA016672"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"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 RNA-processing mechanism on the 3\u2032 terminus that generates distinct isoforms of mRNAs and\/or other RNA polymerase II transcripts with different 3\u2032UTR lengths. Widespread APA affects post-transcriptional gene regulation in mRNA translation, stability, and localization, and exhibits strong tissue specificity. However, no existing database provides comprehensive information about APA events in a large number of human normal tissues. Using the RNA-seq data from the Genotype-Tissue Expression project, we systematically identified APA events from 9475 samples across 53 human tissues and examined their associations with multiple traits and gene expression across tissues. We further developed APAatlas, a user-friendly database (https:\/\/hanlab.uth.edu\/apa\/) for searching, browsing and downloading related information. APAatlas will help the biomedical research community elucidate the functions and mechanisms of APA events in human tissues.<\/jats:p>","DOI":"10.1093\/nar\/gkz876","type":"journal-article","created":{"date-parts":[[2019,9,30]],"date-time":"2019-09-30T07:17:51Z","timestamp":1569827871000},"page":"D34-D39","source":"Crossref","is-referenced-by-count":51,"title":["APAatlas: decoding alternative polyadenylation across human tissues"],"prefix":"10.1093","volume":"48","author":[{"given":"Wei","family":"Hong","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Hang","family":"Ruan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Zhao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Youqiong","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Yaoming","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Shengli","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Ying","family":"Jing","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Huiwen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]},{"given":"Lixia","family":"Diao","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]},{"given":"Han","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7380-2640","authenticated-orcid":false,"given":"Leng","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"},{"name":"Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,10,5]]},"reference":[{"key":"2020010521381764700_B1","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. Cell Biol."},{"key":"2020010521381764700_B2","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/nmeth.2288","article-title":"Analysis of alternative cleavage and polyadenylation by 3\u2032 region extraction and deep sequencing","volume":"10","author":"Hoque","year":"2013","journal-title":"Nat. Methods"},{"key":"2020010521381764700_B3","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1101\/gad.229328.113","article-title":"Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression","volume":"27","author":"Lianoglou","year":"2013","journal-title":"Genes Dev."},{"key":"2020010521381764700_B4","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1101\/gr.146886.112","article-title":"Widespread and extensive lengthening of 3\u2032 UTRs in the mammalian brain","volume":"23","author":"Miura","year":"2013","journal-title":"Genome Res."},{"key":"2020010521381764700_B5","doi-asserted-by":"crossref","first-page":"R100","DOI":"10.1186\/gb-2005-6-12-r100","article-title":"Biased alternative polyadenylation in human tissues","volume":"6","author":"Zhang","year":"2005","journal-title":"Genome Biol."},{"key":"2020010521381764700_B6","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1126\/science.1155390","article-title":"Proliferating cells express mRNAs with shortened 3\u2032 untranslated regions and fewer MicroRNA target sites","volume":"320","author":"Sandberg","year":"2008","journal-title":"Science"},{"key":"2020010521381764700_B7","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s40484-018-0148-3","article-title":"Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data","volume":"6","author":"Guvenek","year":"2018","journal-title":"Quant. Biol."},{"key":"2020010521381764700_B8","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1038\/nature13261","article-title":"CFIm25 links alternative polyadenylation to glioblastoma tumour suppression","volume":"510","author":"Masamha","year":"2014","journal-title":"Nature"},{"key":"2020010521381764700_B9","doi-asserted-by":"crossref","first-page":"5274","DOI":"10.1038\/ncomms6274","article-title":"Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3\u2032-UTR landscape across seven tumour types","volume":"5","author":"Xia","year":"2014","journal-title":"Nat. Commun."},{"key":"2020010521381764700_B10","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1093\/jnci\/djx223","article-title":"Comprehensive characterization of alternative polyadenylation in human cancer","volume":"110","author":"Xiang","year":"2018","journal-title":"JNCI J. Natl. Cancer Inst."},{"key":"2020010521381764700_B11","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.trecan.2018.09.009","article-title":"Maximizing the utility of cancer transcriptomic data","volume":"4","author":"Xiang","year":"2018","journal-title":"Trends Cancer"},{"key":"2020010521381764700_B12","doi-asserted-by":"crossref","first-page":"D165","DOI":"10.1093\/nar\/gkl870","article-title":"PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes","volume":"35","author":"Lee","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B13","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/bti589","article-title":"PACdb: PolyA cleavage site and 3\u2032-UTR database","volume":"21","author":"Brockman","year":"2005","journal-title":"Bioinformatics"},{"key":"2020010521381764700_B14","doi-asserted-by":"crossref","first-page":"bau076","DOI":"10.1093\/database\/bau076","article-title":"APADB: a database for alternative polyadenylation and microRNA regulation events","volume":"2014","author":"M\u00fcller","year":"2014","journal-title":"Database"},{"key":"2020010521381764700_B15","doi-asserted-by":"crossref","first-page":"D59","DOI":"10.1093\/nar\/gku1076","article-title":"APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals","volume":"43","author":"You","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B16","doi-asserted-by":"crossref","first-page":"D315","DOI":"10.1093\/nar\/gkx1000","article-title":"PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes","volume":"46","author":"Wang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B17","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/s41576-019-0145-z","article-title":"Alternative cleavage and polyadenylation in health and disease","volume":"20","author":"Gruber","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"2020010521381764700_B18","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1261\/rna.046037.114","article-title":"IsoSCM: improved and alternative 3\u2032 UTR annotation using multiple change-point inference","volume":"21","author":"Shenker","year":"2015","journal-title":"RNA"},{"key":"2020010521381764700_B19","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13059-018-1414-4","article-title":"QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data","volume":"19","author":"Ha","year":"2018","journal-title":"Genome Biol"},{"key":"2020010521381764700_B20","doi-asserted-by":"crossref","first-page":"D1027","DOI":"10.1093\/nar\/gkx892","article-title":"TC3A: the cancer 3\u2032 UTR atlas","volume":"46","author":"Feng","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B21","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The Genotype-Tissue Expression (GTEx) project","volume":"45","author":"Lonsdale","year":"2013","journal-title":"Nat. Genet."},{"key":"2020010521381764700_B22","doi-asserted-by":"crossref","first-page":"D975","DOI":"10.1093\/nar\/gkt1211","article-title":"NCBI\u2019s database of genotypes and phenotypes: dbGaP","volume":"42","author":"Tryka","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B23","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gkr854","article-title":"The sequence read archive: explosive growth of sequencing data","volume":"40","author":"Kodama","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B24","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1126\/science.aaa0355","article-title":"The human transcriptome across tissues and individuals","volume":"348","author":"Mel\u00e9","year":"2015","journal-title":"Science"},{"key":"2020010521381764700_B25","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"2020010521381764700_B26","doi-asserted-by":"crossref","first-page":"D766","DOI":"10.1093\/nar\/gky955","article-title":"GENCODE reference annotation for the human and mouse genomes","volume":"47","author":"Frankish","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B27","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B28","doi-asserted-by":"crossref","first-page":"D745","DOI":"10.1093\/nar\/gky1113","article-title":"Ensembl 2019","volume":"47","author":"Cunningham","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521381764700_B29","doi-asserted-by":"crossref","first-page":"e1005166","DOI":"10.1371\/journal.pgen.1005166","article-title":"Systematic profiling of Poly(A)+ transcripts modulated by core 3\u2032 end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation","volume":"11","author":"Li","year":"2015","journal-title":"PLOS Genet."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D34\/31698024\/gkz876.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D34\/31698024\/gkz876.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,23]],"date-time":"2021-01-23T18:35:19Z","timestamp":1611426919000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D34\/5581730"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,5]]},"references-count":29,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2019,10,5]]},"published-print":{"date-parts":[[2020,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz876","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":[[2019,10,5]]}}}