{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T20:25:19Z","timestamp":1777580719019,"version":"3.51.4"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,10,18]],"date-time":"2016-10-18T00:00:00Z","timestamp":1476748800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,10,18]],"date-time":"2016-10-18T00:00:00Z","timestamp":1476748800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications in the length of 3\u2019UTRs have been found to play an important role in this context, since alternative 3\u2019 UTRs could lead to differences for example in regulation by microRNAs and cellular localization of the transcripts thus altering their fate.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We propose a strategy to identify the genes undergoing regulation of 3\u2019 UTR length using RNA sequencing data obtained from standard libraries, thus widely applicable to data originally obtained to perform classical differential expression analyses. We decided to exploit previously annotated APA sites from public databases, in contrast with other approaches recently proposed in which the location of the APA site is inferred from the data together with the relative abundance of the isoforms.<\/jats:p>\n                <jats:p>We demonstrate the reliability of our method by comparing it to the results of other microarray based or specific RNA-seq libraries methods and show that using APA sites databases results in higher sensitivity compared to de novo site prediction approach.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>We implemented the algorithm in a Bioconductor package to facilitate its broad usage in the scientific community. The ability of this approach to detect shortening from libraries with a number of reads comparable to that needed for differential expression analyses makes it useful for investigating if alternative polyadenylation is relevant in a certain biological process without requiring specific experimental assays.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1254-8","type":"journal-article","created":{"date-parts":[[2016,10,18]],"date-time":"2016-10-18T14:20:20Z","timestamp":1476800420000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":51,"title":["Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries"],"prefix":"10.1186","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1066-927X","authenticated-orcid":false,"given":"Elena","family":"Grassi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elisa","family":"Mariella","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio","family":"Lembo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivan","family":"Molineris","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Provero","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,10,18]]},"reference":[{"issue":"6","key":"1254_CR1","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1016\/j.tibs.2013.03.005","volume":"38","author":"B Tian","year":"2013","unstructured":"Tian B, Manley JL. Alternative cleavage and polyadenylation: the long and short of it,. Trends Biochem Sci. 2013; 38(6):312\u201320. doi:10.1016\/j.tibs.2013.03.005.","journal-title":"Trends Biochem Sci"},{"issue":"17","key":"1254_CR2","doi-asserted-by":"publisher","first-page":"1770","DOI":"10.1101\/gad.17268411","volume":"25","author":"NJ Proudfoot","year":"2011","unstructured":"Proudfoot NJ. Ending the message: poly(A) signals then and now. Gene Dev. 2011; 25(17):1770\u201382. doi:10.1101\/gad.17268411.","journal-title":"Gene Dev"},{"issue":"7","key":"1254_CR3","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/nrg3482","volume":"14","author":"R Elkon","year":"2013","unstructured":"Elkon R, Ugalde AP, Agami R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet. 2013; 14(7):496\u2013506. doi:10.1038\/nrg3482.","journal-title":"Nat Rev Genet"},{"issue":"12","key":"1254_CR4","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/gb-2005-6-12-r100","volume":"6","author":"H Zhang","year":"2005","unstructured":"Zhang H, Lee JY, Tian B. Biased alternative polyadenylation in human tissues,. Genome Biol. 2005; 6(12):100. doi:10.1186\/gb-2005-6-12-r100.","journal-title":"Genome Biol"},{"issue":"21","key":"1254_CR5","doi-asserted-by":"publisher","first-page":"2380","DOI":"10.1101\/gad.229328.113","volume":"27","author":"S Lianoglou","year":"2013","unstructured":"Lianoglou S, Garg V, Yang JL, Leslie CS, Mayr C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression,. Gene Dev. 2013; 27(21):2380\u201396. doi:10.1101\/gad.229328.113.","journal-title":"Gene Dev"},{"issue":"7468","key":"1254_CR6","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/nature12531","volume":"501","author":"T Lappalainen","year":"2013","unstructured":"Lappalainen T, Sammeth M, Friedl\u00e4nder MR, \u2019t Hoen PaC, Monlong J, Rivas Ma, Gonz\u00e0lez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Alml\u00f6f J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HPJ, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, H\u00e4sler R, Syv\u00e4nen AC, van Ommen G-J, Brazma A, Meitinger T, Rosenstiel P, Guig\u00f3 R, Gut IG, Estivill X, Dermitzakis ET, Palotie A, Deleuze JF, Gyllensten U, Brunner H, Veltman J, Cambon-Thomsen A, Mangion J, Bentley D, Hamosh A, \u2018t Hoen PaC, Monlong J, Rivas Ma, Gonz\u00e0lez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Alml\u00f6f J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HPJ, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Lehrach H, Schreiber S, Sudbrak R, Carracedo \u00c1, Antonarakis SE, H\u00e4sler R, Syv\u00e4nen AC, van Ommen G-J, Brazma A, Meitinger T, Rosenstiel P, Guig\u00f3 R, Gut IG, Estivill X, Dermitzakis ET. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013; 501(7468):506\u201311. doi:10.1038\/nature12531.","journal-title":"Nature"},{"issue":"5","key":"1254_CR7","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1101\/gad.276477.115","volume":"30","author":"M M\u00fcller-McNicoll","year":"2016","unstructured":"M\u00fcller-McNicoll M, Botti V, de Jesus Domingues AM, Brandl H, Schwich OD, Steiner MC, Curk T, Poser I, Zarnack K, Neugebauer KM. SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export,. Gene Dev. 2016; 30(5):553\u201366. doi:10.1101\/gad.276477.115.","journal-title":"Gene Dev"},{"issue":"5883","key":"1254_CR8","doi-asserted-by":"publisher","first-page":"1643","DOI":"10.1126\/science.1155390","volume":"320","author":"R Sandberg","year":"2008","unstructured":"Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating Cells Express mRNAs with Shortened 3\u2019 Untranslated Regions and Fewer MicroRNA Target Sites. Science. 2008; 320(5883):1643\u20137. doi:10.1126\/science.1155390.","journal-title":"Science"},{"issue":"4","key":"1254_CR9","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1016\/j.cell.2009.06.016","volume":"138","author":"C Mayr","year":"2009","unstructured":"Mayr C, Bartel DP. Widespread Shortening of 3\u2019UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells. Cell. 2009; 138(4):673\u201384. doi:10.1016\/j.cell.2009.06.016.","journal-title":"Cell"},{"issue":"17","key":"1254_CR10","doi-asserted-by":"publisher","first-page":"7028","DOI":"10.1073\/pnas.0900028106","volume":"106","author":"Z Ji","year":"2009","unstructured":"Ji Z, Lee JY, Pan Z, Jiang B, Tian B. Progressive lengthening of 3\u2019 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A. 2009; 106(17):7028\u201333. doi:s10.1073\/pnas.0900028106.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"1254_CR11","doi-asserted-by":"publisher","first-page":"31129","DOI":"10.1371\/journal.pone.0031129","volume":"7","author":"A Lembo","year":"2012","unstructured":"Lembo A, Di Cunto F, Provero P. Shortening of 3\u2019UTRs correlates with poor prognosis in breast and lung cancer. PloS one. 2012; 7(2):31129. doi:10.1371\/journal.pone.0031129.","journal-title":"PloS one"},{"key":"1254_CR12","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1007\/978-1-4939-1221-6_3","volume":"825","author":"D Zheng","year":"2014","unstructured":"Zheng D, Tian B. RNA-binding proteins in regulation of alternative cleavage and polyadenylation. Adv Exp Med Biol. 2014; 825:97\u2013127. doi:http:\/\/dx.doi.org\/10.1007\/978-1-4939-1221-6_3.","journal-title":"Adv Exp Med Biol"},{"issue":"5","key":"1254_CR13","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1101\/gr.115295.110","volume":"21","author":"Y Fu","year":"2011","unstructured":"Fu Y, Sun Y, Li Y, Li J, Rao X, Chen C, Xu A. Differential genome-wide profiling of tandem 3\u2019 UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res. 2011; 21(5):741\u20137. doi:10.1101\/gr.115295.110.","journal-title":"Genome Res"},{"issue":"Database-Issue","key":"1254_CR14","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1093\/nar\/gkl870","volume":"35","author":"JY Lee","year":"2007","unstructured":"Lee JY, Yeh I, Park JY, Tian B. Polya_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 2007; 35(Database-Issue):165\u20138. doi:10.1093\/nar\/gkl870.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1254_CR15","first-page":"59","volume":"43","author":"L You","year":"2014","unstructured":"You L, Wu J, Feng Y, Fu Y, Guo Y, Long L, Zhang H, Luan Y, Tian P, Chen L, Huang G, Huang S, Li Y, Li J, Chen C, Zhang Y, Chen S, Xu A. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals,. Nucleic Acids Res. 2014; 43(Database issue):59\u201367. doi:10.1093\/nar\/gku1076.","journal-title":"Nucleic Acids Res"},{"issue":"7505","key":"1254_CR16","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1038\/nature13261","volume":"509","author":"CP Masamha","year":"2014","unstructured":"Masamha CP, Xia Z, Yang J, Albrecht TR, Li M, Shyu AB, Li W, Wagner EJ. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature. 2014; 509(7505):412\u20136. doi:10.1038\/nature13261.","journal-title":"Nature"},{"issue":"3","key":"1254_CR17","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1261\/rna.035360.112","volume":"19","author":"L Wang","year":"2013","unstructured":"Wang L, Dowell RD, Yi R. Genome-wide maps of polyadenylation reveal dynamic mRNA 3\u2019-end formation in mammalian cell lineages. RNA. 2013; 19(3):413\u201325. doi:10.1261\/rna.035360.112.","journal-title":"RNA"},{"issue":"2","key":"1254_CR18","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1016\/j.gene.2013.06.052","volume":"527","author":"J Lu","year":"2013","unstructured":"Lu J, Bushel PR. Dynamic expression of 3\u2019 UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: Implications in gene expression profiling. Gene. 2013; 527(2):616\u201323. doi:10.1016\/j.gene.2013.06.052.","journal-title":"Gene"},{"issue":"11","key":"1254_CR19","doi-asserted-by":"publisher","first-page":"1845","DOI":"10.1093\/bioinformatics\/btv035","volume":"31","author":"L Le Pera","year":"2015","unstructured":"Le Pera L, Mazzapioda M, Tramontano A. 3USS: a web server for detecting alternative 3\u2019utrs from rna-seq experiments. Bioinformatics. 2015; 31(11):1845\u20131847. doi:10.1093\/bioinformatics\/btv035.","journal-title":"Bioinformatics"},{"issue":"15","key":"1254_CR20","doi-asserted-by":"publisher","first-page":"2162","DOI":"10.1093\/bioinformatics\/btu189","volume":"30","author":"W Wang","year":"2014","unstructured":"Wang W, Wei Z, Li H. A change-point model for identifying 3\u2019UTR switching by next-generation RNA sequencing. Bioinformatics. 2014; 30(15):2162\u2013170. doi:10.1093\/bioinformatics\/btu189.","journal-title":"Bioinformatics"},{"key":"1254_CR21","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.ymeth.2015.04.011","volume":"83","author":"M Kim","year":"2015","unstructured":"Kim M, You BH, Nam JW. Global estimation of the 3\u2019 untranslated region landscape using RNA sequencing. Methods. 2015; 83:111\u20137. doi:10.1016\/j.ymeth.2015.04.011.","journal-title":"Methods"},{"issue":"1","key":"1254_CR22","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1261\/rna.046037.114","volume":"21","author":"S Shenker","year":"2015","unstructured":"Shenker S, Miura P, Sanfilippo P, Lai EC. IsoSCM: improved and alternative 3\u2019 UTR annotation using multiple change-point inference,. RNA (New York, NY). 2015; 21(1):14\u201327. doi:10.1261\/rna.046037.114.","journal-title":"RNA (New York, NY)"},{"key":"1254_CR23","doi-asserted-by":"crossref","unstructured":"Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A. KLEAT: cleavage site analysis of transcriptomes. In: Biocomputing 2015: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 4-8, 2015: 2015. p. 347\u201358. doi:10.1142\/9789814644730_0034. http:\/\/psb.stanford.edu\/psb-online\/proceedings\/psb2015\/birol.pdf.","DOI":"10.1142\/9789814644730_0034"},{"issue":"1","key":"1254_CR24","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1038\/msb.2011.69","volume":"7","author":"Z Ji","year":"2011","unstructured":"Ji Z, Luo W, Li W, Hoque M, Pan Z, Zhao Y, Tian B. Transcriptional activity regulates alternative cleavage and polyadenylation. Mol Syst Biol. 2011; 7(1):534. doi:10.1038\/msb.2011.69.","journal-title":"Mol Syst Biol"},{"issue":"7221","key":"1254_CR25","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/nature07509","volume":"456","author":"ET Wang","year":"2008","unstructured":"Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes,. Nature. 2008; 456(7221):470\u20136. doi:10.1038\/nature07509.","journal-title":"Nature"},{"key":"1254_CR26","volume-title":"Statistical Methods for Research Workers","author":"RA Fisher","year":"1925","unstructured":"Fisher RA. Statistical Methods for Research Workers. Edinburgh: Oliver & Boyd; 1925. doi:10.1002\/qj.49708235130."},{"issue":"Database Issue","key":"1254_CR27","first-page":"717","volume":"44","author":"ML Speir","year":"2015","unstructured":"Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC genome browser database: 2016 update. Nucleic Acids Res. 2015; 44(Database Issue):717\u201325. doi:10.1093\/nar\/gkv1275.","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"1254_CR28","first-page":"501","volume":"33","author":"KD Pruitt","year":"2005","unstructured":"Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005; 33(suppl 1):501\u20134. doi:10.1093\/nar\/gki025.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"1254_CR29","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ. BLAT\u2013the BLAST-like alignment tool. Genome Res. 2002; 12(4):656\u201364. doi:10.1101\/gr.229202.","journal-title":"Genome Res"},{"issue":"2","key":"1254_CR30","doi-asserted-by":"publisher","first-page":"1005879","DOI":"10.1371\/journal.pgen.1005879","volume":"12","author":"Y Hoffman","year":"2016","unstructured":"Hoffman Y, Bublik DR, Ugalde, Elkon R, Biniashvili T, Agami R, Oren M, Pilpel Y. 3\u2019UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells. PLoS Genet. 2016; 12(2):1005879. doi:10.1371\/journal.pgen.1005879.","journal-title":"PLoS Genet"},{"key":"1254_CR31","unstructured":"Roar wiki on github. https:\/\/github.com\/vodkatad\/roar\/wiki\/Identify-differential-APA-usage-from-RNA-seq-alignments."},{"issue":"7369","key":"1254_CR32","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/nature10532","volume":"478","author":"D Brawand","year":"2011","unstructured":"Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grutzner F, Bergmann S, Nielsen R, Paabo S, Kaessmann H. The evolution of gene expression levels in mammalian organs. Nature. 2011; 478(7369):343\u20138. doi:10.1038\/nature10532.","journal-title":"Nature"},{"key":"1254_CR33","unstructured":"Kaessmann H. GEO dataset GSE30352, runs: SRR306857, SRR306858, SRR306838, SRR306839, SRR306840, SRR306841, SRR306842, SRR306843. 2011."},{"key":"1254_CR34","unstructured":"Roth R. GEO dataset GSE3526. 2006."},{"issue":"2","key":"1254_CR35","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1007\/s10048-006-0032-6","volume":"7","author":"RB Roth","year":"2006","unstructured":"Roth RB, Hevezi P, Lee J, Willhite D, Lechner SM, Foster AC, Zlotnik A. Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics. 2006; 7(2):67\u201380. doi:10.1007\/s10048-006-0032-6.","journal-title":"Neurogenetics"},{"key":"1254_CR36","unstructured":"Stephan D, Liang W. GEO dataset GSE5281. 2006."},{"issue":"3","key":"1254_CR37","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1152\/physiolgenomics.00208.2006","volume":"28","author":"WS Liang","year":"2007","unstructured":"Liang WS, Dunckley T, Beach TG, Grover A, Mastroeni D, Walker DG, Caselli RJ, Kukull WA, McKeel D, Morris JC, Hulette C, Schmechel D, Alexander GE, Reiman EM, Rogers J, Stephan DA. Gene expression profiles in anatomically and functionally distinct regions of the normal aged human brain. Physiol Genomics. 2007; 28(3):311\u201322. doi:10.1152\/physiolgenomics.00208.2006.","journal-title":"Physiol Genomics"},{"key":"1254_CR38","unstructured":"Roth R. GEO dataset GSE7307. 2007."},{"key":"1254_CR39","unstructured":"Ffrench-Mullen J. GEO dataset GSE7621. 2007."},{"issue":"6","key":"1254_CR40","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1371\/journal.pgen.0030098","volume":"3","author":"TG Lesnick","year":"2007","unstructured":"Lesnick TG, Papapetropoulos S, Mash DC, Ffrench-Mullen J, Shehadeh L, de Andrade M, Henley JR, Rocca WA, Ahlskog JE, Maraganore DM. A genomic pathway approach to a complex disease: axon guidance and Parkinson disease. PLoS Genet. 2007; 3(6):98. doi:10.1371\/journal.pgen.0030098.","journal-title":"PLoS Genet"},{"key":"1254_CR41","doi-asserted-by":"crossref","unstructured":"Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L, Schroth GP, Perez EA, Thompson EA. Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing. Plos One. 2011; 6. doi:10.1371\/journal.pone.0017490.","DOI":"10.1371\/journal.pone.0017490"},{"key":"1254_CR42","unstructured":"Sun Z. GEO dataset GSE27003, runs: SRR097788, SRR097789, SRR097790. 2011."},{"key":"1254_CR43","unstructured":"ENCODE RNAseq Standards. 2011. https:\/\/genome.ucsc.edu\/ENCODE\/protocols\/dataStandards\/."},{"issue":"1","key":"1254_CR44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2407-3-13","volume":"3","author":"M Nugoli","year":"2003","unstructured":"Nugoli M, Chuchana P, Vendrell J, Orsetti B, Ursule L, Nguyen C, Birnbaum D, Douzery EJ, Cohen P, Theillet C. Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications. BMC Cancer. 2003; 3(1):1\u201312. doi:10.1186\/1471-2407-3-13.","journal-title":"BMC Cancer"},{"issue":"6","key":"1254_CR45","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1093\/bib\/bbs046","volume":"14","author":"MA Dillies","year":"2013","unstructured":"Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Lalo\u00eb D, Le Gall C, Scha\u00ebffer B, Le Crom S, Guedj M, Jaffr\u00e9zic F. A comprehensive evaluation of normalization methods for illumina high-throughput RNA sequencing data analysis. Brief Bioinform. 2013; 14(6):671\u201383. doi:10.1093\/bib\/bbs046.","journal-title":"Brief Bioinform"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1254-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1254-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1254-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T17:59:46Z","timestamp":1706810386000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1254-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10,18]]},"references-count":45,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1254"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1254-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,10,18]]},"assertion":[{"value":"30 March 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 October 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"423"}}