{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T06:10:10Z","timestamp":1790403010453,"version":"4.1.0"},"reference-count":107,"publisher":"Elsevier BV","issue":"12","license":[{"start":{"date-parts":[[2019,12,1]],"date-time":"2019-12-01T00:00:00Z","timestamp":1575158400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2019,12,1]],"date-time":"2019-12-01T00:00:00Z","timestamp":1575158400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2019,11,20]],"date-time":"2019-11-20T00:00:00Z","timestamp":1574208000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1016\/j.celrep.2019.11.077","type":"journal-article","created":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T10:43:42Z","timestamp":1576579422000},"page":"4069-4085.e6","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":79,"title":["Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids"],"prefix":"10.1016","volume":"29","author":[{"given":"Jitu Wilson","family":"George","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huihui","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler James","family":"Carpenter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly Katherine","family":"Foy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anindita","family":"Chatterjee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda Lynn","family":"Patterson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Koeman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Adams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary Brian","family":"Madaj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Chesla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erica Elizabeth","family":"Marsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy Junius","family":"Triche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9767-4084","authenticated-orcid":false,"given":"Hui","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Manuel","family":"Teixeira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2019.11.077_bib1","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.celrep.2012.12.008","article-title":"Deciphering signatures of mutational processes operative in human cancer","volume":"3","author":"Alexandrov","year":"2013","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2019.11.077_bib105","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics."},{"key":"10.1016\/j.celrep.2019.11.077_bib2","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1093\/humrep\/deh698","article-title":"Gene expression studies provide clues to the pathogenesis of uterine leiomyoma: new evidence and a systematic review","volume":"20","author":"Arslan","year":"2005","journal-title":"Hum. Reprod."},{"key":"10.1016\/j.celrep.2019.11.077_bib3","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/0092-8674(95)90052-7","article-title":"Disruption of the architectural factor HMGI-C: DNA-binding AT hook motifs fused in lipomas to distinct transcriptional regulatory domains","volume":"82","author":"Ashar","year":"1995","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2019.11.077_bib4","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1097\/01.EDE.0000054360.61254.27","article-title":"Why is parity protective for uterine fibroids?","volume":"14","author":"Baird","year":"2003","journal-title":"Epidemiology"},{"key":"10.1016\/j.celrep.2019.11.077_bib5","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1002\/1097-4652(2000)9999:999<000::AID-JCP1040>3.0.CO;2-E","article-title":"17-beta estradiol elicits an autocrine leiomyoma cell proliferation: evidence for a stimulation of protein kinase-dependent pathway","volume":"186","author":"Barbarisi","year":"2001","journal-title":"J.\u00a0Cell. Physiol."},{"key":"10.1016\/j.celrep.2019.11.077_bib6","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","year":"2018","journal-title":"Nat. Biotechnol."},{"issue":"8, Suppl","key":"10.1016\/j.celrep.2019.11.077_bib7","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1177\/1933719107309591","article-title":"Thrombospondin-1 and thrombospondin-2 mRNA and TSP-1 and TSP-2 protein expression in uterine fibroids and correlation to the genes COL1A1 and COL3A1 and to the collagen cross-link hydroxyproline","volume":"14","author":"Behera","year":"2007","journal-title":"Reprod. Sci."},{"key":"10.1016\/j.celrep.2019.11.077_bib8","doi-asserted-by":"crossref","first-page":"5473","DOI":"10.1073\/pnas.1418631112","article-title":"Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants","volume":"112","author":"Belkadi","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2019.11.077_bib9","first-page":"E1112","article-title":"Estrogen receptors (ERalpha\/ERbeta) in normal and pathological growth of the human myometrium: pregnancy and leiomyoma","volume":"276","author":"Benassayag","year":"1999","journal-title":"Am. J. Physiol."},{"key":"10.1016\/j.celrep.2019.11.077_bib10","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/modpathol.2013.243","article-title":"MED12 and HMGA2 mutations: two independent genetic events in uterine leiomyoma and leiomyosarcoma","volume":"27","author":"Bertsch","year":"2014","journal-title":"Mod. Pathol."},{"key":"10.1016\/j.celrep.2019.11.077_bib11","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1210\/endo-59-2-165","article-title":"Inhibitory action of desoxycorticosterone acetate, cortisone acetate, and testosterone on uterine growth induced by estradiol-17beta","volume":"59","author":"Bever","year":"1956","journal-title":"Endocrinology"},{"key":"10.1016\/j.celrep.2019.11.077_bib12","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1210\/endo-80-3-423","article-title":"Differential inhibition by cortisol of estrogen-stimulated uterine responses","volume":"80","author":"Bitman","year":"1967","journal-title":"Endocrinology"},{"key":"10.1016\/j.celrep.2019.11.077_bib13","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.cell.2005.08.020","article-title":"Core transcriptional regulatory circuitry in human embryonic stem cells","volume":"122","author":"Boyer","year":"2005","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2019.11.077_bib98","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btx373","article-title":"FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool","author":"Brown","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2019.11.077_bib14","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1056\/NEJMra1209993","article-title":"Uterine fibroids","volume":"369","author":"Bulun","year":"2013","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.celrep.2019.11.077_bib15","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1016\/j.molcel.2013.01.038","article-title":"Modification of enhancer chromatin: what, how, and why?","volume":"49","author":"Calo","year":"2013","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2019.11.077_bib16","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1097\/01.LAB.0000017499.51216.3E","article-title":"Immortalization of human uterine leiomyoma and myometrial cell lines after induction of telomerase activity: molecular and phenotypic characteristics","volume":"82","author":"Carney","year":"2002","journal-title":"Lab. Invest."},{"key":"10.1016\/j.celrep.2019.11.077_bib17","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1093\/humrep\/15.7.1469","article-title":"An immunohistochemical analysis of fibroid vasculature","volume":"15","author":"Casey","year":"2000","journal-title":"Hum. Reprod."},{"key":"10.1016\/j.celrep.2019.11.077_bib18","first-page":"514","article-title":"Endocrine and paracrine regulation of birth at term and preterm","volume":"21","author":"Challis","year":"2000","journal-title":"Endocr. Rev."},{"key":"10.1016\/j.celrep.2019.11.077_bib19","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s13073-017-0424-2","article-title":"Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden","volume":"9","author":"Chalmers","year":"2017","journal-title":"Genome Med."},{"key":"10.1016\/j.celrep.2019.11.077_bib20","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1177\/1933719109348924","article-title":"Uterine leiomyomas exhibit fewer stem\/progenitor cell characteristics when compared with corresponding normal myometrium","volume":"17","author":"Chang","year":"2010","journal-title":"Reprod. Sci."},{"key":"10.1016\/j.celrep.2019.11.077_bib21","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1021\/bi901881c","article-title":"DNA bending by the mammalian high-mobility group protein AT hook 2","volume":"49","author":"Chen","year":"2010","journal-title":"Biochemistry"},{"key":"10.1016\/j.celrep.2019.11.077_bib22","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/humupd\/dmv030","article-title":"Epidemiological and genetic clues for molecular mechanisms involved in uterine leiomyoma development and growth","volume":"21","author":"Commandeur","year":"2015","journal-title":"Hum. Reprod. Update"},{"key":"10.1016\/j.celrep.2019.11.077_bib104","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner.","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics."},{"key":"10.1016\/j.celrep.2019.11.077_bib23","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2019.11.077_bib24","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1210\/er.2005-0018","article-title":"Endocrine regulation of HOX genes","volume":"27","author":"Daftary","year":"2006","journal-title":"Endocr. Rev."},{"key":"10.1016\/j.celrep.2019.11.077_bib99","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics."},{"key":"10.1016\/j.celrep.2019.11.077_bib25","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s13059-015-0741-y","article-title":"Reconstructing A\/B compartments as revealed by Hi-C using long-range correlations in epigenetic data","volume":"16","author":"Fortin","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2019.11.077_bib26","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1002\/humu.22033","article-title":"Detecting false-positive signals in exome sequencing","volume":"33","author":"Fuentes Fajardo","year":"2012","journal-title":"Hum. Mutat."},{"key":"10.1016\/j.celrep.2019.11.077_bib27","doi-asserted-by":"crossref","first-page":"3673","DOI":"10.1093\/bioinformatics\/btv408","article-title":"SomaticSignatures: inferring mutational signatures from single-nucleotide variants","volume":"31","author":"Gehring","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2019.11.077_bib28","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1038\/s41598-017-01199-0","article-title":"Multiple clinical characteristics separate MED12-mutation-positive and -negative uterine leiomyomas","volume":"7","author":"Heinonen","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2019.11.077_bib29","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1093\/molehr\/5.12.1150","article-title":"Chromosomal translocations affecting 12q14-15 but not deletions of the long arm of chromosome 7 associated with a growth advantage of uterine smooth muscle cells","volume":"5","author":"Hennig","year":"1999","journal-title":"Mol. Hum. Reprod."},{"key":"10.1016\/j.celrep.2019.11.077_bib30","doi-asserted-by":"crossref","first-page":"21","DOI":"10.2353\/ajpath.2010.090999","article-title":"Epigenetic regulation of myofibroblast differentiation by DNA methylation","volume":"177","author":"Hu","year":"2010","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.celrep.2019.11.077_bib31","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1210\/en.2009-1225","article-title":"Progesterone is essential for maintenance and growth of uterine leiomyoma","volume":"151","author":"Ishikawa","year":"2010","journal-title":"Endocrinology"},{"key":"10.1016\/j.celrep.2019.11.077_bib32","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1210\/jc.2012-3237","article-title":"Uterine leiomyoma: available medical treatments and new possible therapeutic options","volume":"98","author":"Islam","year":"2013","journal-title":"J.\u00a0Clin. Endocrinol. Metab."},{"key":"10.1016\/j.celrep.2019.11.077_bib33","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1016\/j.ajog.2010.02.039","article-title":"Racial and ethnic disparities in benign gynecologic conditions and associated surgeries","volume":"202","author":"Jacoby","year":"2010","journal-title":"Am. J. Obstet. Gynecol."},{"key":"10.1016\/j.celrep.2019.11.077_bib34","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nrg3230","article-title":"Functions of DNA methylation: islands, start sites, gene bodies and beyond","volume":"13","author":"Jones","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.celrep.2019.11.077_bib35","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib107","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib36","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/nrg1225","article-title":"Developmental genetics of the female reproductive tract in mammals","volume":"4","author":"Kobayashi","year":"2003","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.celrep.2019.11.077_bib37","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1093\/molehr\/7.11.1085","article-title":"Comparative analysis of cyclin D1 and oestrogen receptor (alpha and beta) levels in human leiomyoma and adjacent myometrium","volume":"7","author":"Kov\u00e1cs","year":"2001","journal-title":"Mol. Hum. Reprod."},{"key":"10.1016\/j.celrep.2019.11.077_bib38","doi-asserted-by":"crossref","first-page":"353297","DOI":"10.1155\/2011\/353297","article-title":"Progesterone interactions with the cervix: translational implications for term and preterm birth","volume":"2011","author":"Larsen","year":"2011","journal-title":"Infect. Dis. Obstet. Gynecol."},{"key":"10.1016\/j.celrep.2019.11.077_bib39","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/nature12213","article-title":"Mutational heterogeneity in cancer and the search for new cancer-associated genes","volume":"499","author":"Lawrence","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2019.11.077_bib40","doi-asserted-by":"crossref","first-page":"783289","DOI":"10.1155\/2014\/783289","article-title":"The extracellular matrix contributes to mechanotransduction in uterine fibroids","volume":"2014","author":"Leppert","year":"2014","journal-title":"Obstet. Gynecol. Int."},{"key":"10.1016\/j.celrep.2019.11.077_bib41","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nature08514","article-title":"Human DNA methylomes at base resolution show widespread epigenomic differences","volume":"462","author":"Lister","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2019.11.077_bib101","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics."},{"key":"10.1016\/j.celrep.2019.11.077_bib102","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools.","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics."},{"key":"10.1016\/j.celrep.2019.11.077_bib42","doi-asserted-by":"crossref","first-page":"1237905","DOI":"10.1126\/science.1237905","article-title":"Global epigenomic reconfiguration during mammalian brain development","volume":"341","author":"Lister","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.celrep.2019.11.077_bib43","doi-asserted-by":"crossref","first-page":"E1512","DOI":"10.1210\/jc.2015-2815","article-title":"HoxA13 Regulates Phenotype Regionalization of Human Pregnant Myometrium","volume":"100","author":"Liu","year":"2015","journal-title":"J.\u00a0Clin. Endocrinol. Metab."},{"key":"10.1016\/j.celrep.2019.11.077_bib44","doi-asserted-by":"crossref","first-page":"e66632","DOI":"10.1371\/journal.pone.0066632","article-title":"Genome-wide DNA methylation analysis reveals a potential mechanism for the pathogenesis and development of uterine leiomyomas","volume":"8","author":"Maekawa","year":"2013","journal-title":"PLoS ONE"},{"key":"10.1016\/j.celrep.2019.11.077_bib45","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1126\/science.1208930","article-title":"MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas","volume":"334","author":"M\u00e4kinen","year":"2011","journal-title":"Science"},{"key":"10.1016\/j.celrep.2019.11.077_bib46","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1055\/s-0030-1251475","article-title":"Why leiomyomas are called fibroids: the central role of extracellular matrix in symptomatic women","volume":"28","author":"Malik","year":"2010","journal-title":"Semin. Reprod. Med."},{"key":"10.1016\/j.celrep.2019.11.077_bib47","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nature09784","article-title":"The Polycomb complex PRC2 and its mark in life","volume":"469","author":"Margueron","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2019.11.077_bib103","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1101\/gr.239244.118","article-title":"Maftools: efficient and comprehensive analysis of somatic variants in cancer","volume":"28","author":"Mayakonda","year":"2018","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib48","doi-asserted-by":"crossref","first-page":"4719","DOI":"10.1158\/0008-5472.CAN-07-6339","article-title":"Lack of hypoxic response in uterine leiomyomas despite severe tissue hypoxia","volume":"68","author":"Mayer","year":"2008","journal-title":"Cancer Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib49","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1056\/NEJMoa1302736","article-title":"Characterization of uterine leiomyomas by whole-genome sequencing","volume":"369","author":"Mehine","year":"2013","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.celrep.2019.11.077_bib50","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/j.fertnstert.2014.06.050","article-title":"Genomics of uterine leiomyomas: insights from high-throughput sequencing","volume":"102","author":"Mehine","year":"2014","journal-title":"Fertil. Steril."},{"key":"10.1016\/j.celrep.2019.11.077_bib100","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib51","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1073\/pnas.1518752113","article-title":"Integrated data analysis reveals uterine leiomyoma subtypes with distinct driver pathways and biomarkers","volume":"113","author":"Mehine","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2019.11.077_bib52","doi-asserted-by":"crossref","first-page":"3280","DOI":"10.1172\/JCI81534","article-title":"Med12 gain-of-function mutation causes leiomyomas and genomic instability","volume":"125","author":"Mittal","year":"2015","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.celrep.2019.11.077_bib53","doi-asserted-by":"crossref","first-page":"219","DOI":"10.4161\/cbt.10.3.12548","article-title":"The role of the miR-200 family in epithelial-mesenchymal transition","volume":"10","author":"Mongroo","year":"2010","journal-title":"Cancer Biol. Ther."},{"key":"10.1016\/j.celrep.2019.11.077_bib54","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1097\/GCO.0000000000000185","article-title":"Endocrinology of uterine fibroids: steroid hormones, stem cells, and genetic contribution","volume":"27","author":"Moravek","year":"2015","journal-title":"Curr. Opin. Obstet. Gynecol."},{"key":"10.1016\/j.celrep.2019.11.077_bib55","doi-asserted-by":"crossref","first-page":"e33284","DOI":"10.1371\/journal.pone.0033284","article-title":"Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma","volume":"7","author":"Navarro","year":"2012","journal-title":"PLoS ONE"},{"key":"10.1016\/j.celrep.2019.11.077_bib56","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1007\/BF00193583","article-title":"Characteristic chromosome abnormalities, including rearrangements of 6p, del(7q),\u00a0+12, and t(12;14), in 44 uterine leiomyomas","volume":"85","author":"Nilbert","year":"1990","journal-title":"Hum. Genet."},{"key":"10.1016\/j.celrep.2019.11.077_bib57","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1177\/1933719109343310","article-title":"Transforming growth factor beta3 regulates the versican variants in the extracellular matrix-rich uterine leiomyomas","volume":"16","author":"Norian","year":"2009","journal-title":"Reprod. Sci."},{"key":"10.1016\/j.celrep.2019.11.077_bib58","doi-asserted-by":"crossref","first-page":"e36935","DOI":"10.1371\/journal.pone.0036935","article-title":"Role of stem cells in human uterine leiomyoma growth","volume":"7","author":"Ono","year":"2012","journal-title":"PLoS ONE"},{"key":"10.1016\/j.celrep.2019.11.077_bib59","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/0020-7292(89)90853-9","article-title":"A comparative study of the estrogen receptor ratio in myometrium and uterine leiomyomas","volume":"29","author":"Otsuka","year":"1989","journal-title":"Int. J. Gynaecol. Obstet."},{"key":"10.1016\/j.celrep.2019.11.077_bib60","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1101\/gad.1640608","article-title":"The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2","volume":"22","author":"Park","year":"2008","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2019.11.077_bib61","doi-asserted-by":"crossref","first-page":"4870","DOI":"10.1074\/jbc.RA118.001725","article-title":"Oncogenic exon 2 mutations in Mediator subunit MED12 disrupt allosteric activation of cyclin C-CDK8\/19","volume":"293","author":"Park","year":"2018","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.celrep.2019.11.077_bib62","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1158\/1541-7786.MCR-07-0370","article-title":"Antiproliferative effects by Let-7 repression of high-mobility group A2 in uterine leiomyoma","volume":"6","author":"Peng","year":"2008","journal-title":"Mol. Cancer Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib63","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1756-8935-8-6","article-title":"De novo identification of differentially methylated regions in the human genome","volume":"8","author":"Peters","year":"2015","journal-title":"Epigenetics Chromatin"},{"key":"10.1016\/j.celrep.2019.11.077_bib64","first-page":"1351","article-title":"Fusion transcripts involving HMGA2 are not a common molecular mechanism in uterine leiomyomata with rearrangements in 12q15","volume":"63","author":"Quade","year":"2003","journal-title":"Cancer Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib65","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1096\/fj.02-1099com","article-title":"Dexamethasone blocks the rapid biological effects of 17beta-estradiol in the rat uterus without antagonizing its global genomic actions","volume":"17","author":"Rhen","year":"2003","journal-title":"FASEB J."},{"key":"10.1016\/j.celrep.2019.11.077_bib66","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2019.11.077_bib67","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cancergencyto.2004.08.025","article-title":"Updates on the cytogenetics and molecular genetics of bone and soft tissue tumors: leiomyoma","volume":"158","author":"Sandberg","year":"2005","journal-title":"Cancer Genet. Cytogenet."},{"key":"10.1016\/j.celrep.2019.11.077_bib68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/(SICI)1098-2264(199609)17:1<1::AID-GCC1>3.0.CO;2-0","article-title":"Translocation breakpoints upstream of the HMGIC gene in uterine leiomyomata suggest dysregulation of this gene by a mechanism different from that in lipomas","volume":"17","author":"Schoenberg Fejzo","year":"1996","journal-title":"Genes Chromosomes Cancer"},{"key":"10.1016\/j.celrep.2019.11.077_bib69","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/ng0895-436","article-title":"Recurrent rearrangements in the high mobility group protein gene, HMGI-C, in benign mesenchymal tumours","volume":"10","author":"Schoenmakers","year":"1995","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2019.11.077_bib70","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nrg3682","article-title":"Transcriptional enhancers: from properties to genome-wide predictions","volume":"15","author":"Shlyueva","year":"2014","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.celrep.2019.11.077_bib71","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1016\/j.molcel.2013.02.013","article-title":"Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put","volume":"49","author":"Simon","year":"2013","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2019.11.077_bib72","first-page":"275","article-title":"Myofibroblasts from diverse pathologic settings are heterogeneous in their content of actin isoforms and intermediate filament proteins","volume":"60","author":"Skalli","year":"1989","journal-title":"Lab. Invest."},{"key":"10.1016\/j.celrep.2019.11.077_bib73","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1089\/jwh.2013.4334","article-title":"The burden of uterine fibroids for African-American women: results of a national survey","volume":"22","author":"Stewart","year":"2013","journal-title":"J.\u00a0Womens Health (Larchmt.)"},{"key":"10.1016\/j.celrep.2019.11.077_bib74","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2019.11.077_bib75","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nrc.2016.62","article-title":"The role of enhancers in cancer","volume":"16","author":"Sur","year":"2016","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.celrep.2019.11.077_bib76","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1002\/1098-2264(2000)9999:9999<::AID-GCC1078>3.0.CO;2-8","article-title":"Evidence for RAD51L1\/HMGIC fusion in the pathogenesis of uterine leiomyoma","volume":"30","author":"Takahashi","year":"2001","journal-title":"Genes Chromosomes Cancer"},{"key":"10.1016\/j.celrep.2019.11.077_bib77","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.1095\/biolreprod57.6.1338","article-title":"A conserved Hox axis in the mouse and human female reproductive system: late establishment and persistent adult expression of the Hoxa cluster genes","volume":"57","author":"Taylor","year":"1997","journal-title":"Biol. Reprod."},{"key":"10.1016\/j.celrep.2019.11.077_bib106","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":"10.1016\/j.celrep.2019.11.077_bib78","series-title":"R: A Language and Environment for Statistical Computing","author":"R Development Core Team","year":"2006"},{"key":"10.1016\/j.celrep.2019.11.077_bib79","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.tem.2010.01.011","article-title":"Cervical remodeling during pregnancy and parturition","volume":"21","author":"Timmons","year":"2010","journal-title":"Trends Endocrinol. Metab."},{"key":"10.1016\/j.celrep.2019.11.077_bib80","doi-asserted-by":"crossref","first-page":"e90","DOI":"10.1093\/nar\/gkt090","article-title":"Low-level processing of Illumina Infinium DNA Methylation BeadArrays","volume":"41","author":"Triche","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib81","doi-asserted-by":"crossref","first-page":"e8697","DOI":"10.1371\/journal.pone.0008697","article-title":"Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells","volume":"5","author":"Vrba","year":"2010","journal-title":"PLoS ONE"},{"key":"10.1016\/j.celrep.2019.11.077_bib82","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1002\/gcc.20415","article-title":"A micro-RNA signature associated with race, tumor size, and target gene activity in human uterine leiomyomas","volume":"46","author":"Wang","year":"2007","journal-title":"Genes Chromosomes Cancer"},{"key":"10.1016\/j.celrep.2019.11.077_bib83","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"},{"key":"10.1016\/j.celrep.2019.11.077_bib84","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1101\/gr.136101.111","article-title":"Widespread plasticity in CTCF occupancy linked to DNA methylation","volume":"22","author":"Wang","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib85","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1101\/gr.139105.112","article-title":"Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors","volume":"22","author":"Wang","year":"2012","journal-title":"Genome Res."},{"issue":"D1","key":"10.1016\/j.celrep.2019.11.077_bib86","doi-asserted-by":"crossref","first-page":"D172","DOI":"10.1093\/nar\/gkv1243","article-title":"SEA: a super-enhancer archive","volume":"44","author":"Wei","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib87","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/ng1941","article-title":"Epigenetic stem cell signature in cancer","volume":"39","author":"Widschwendter","year":"2007","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2019.11.077_bib88","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btq170","article-title":"ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking","volume":"26","author":"Wilkerson","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2019.11.077_bib89","first-page":"45","article-title":"Changes in the cervical extracellular matrix during pregnancy and parturition","volume":"27","author":"Winkler","year":"1999","journal-title":"J.\u00a0Perinat. Med."},{"key":"10.1016\/j.celrep.2019.11.077_bib90","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1097\/01.AOG.0000285997.38553.4b","article-title":"Hysterectomy rates in the United States, 2003","volume":"110","author":"Wu","year":"2007","journal-title":"Obstet. Gynecol."},{"key":"10.1016\/j.celrep.2019.11.077_bib91","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1095\/biolreprod.115.134924","article-title":"The Polycomb Group Protein EZH2 Impairs DNA Damage Repair Gene Expression in Human Uterine Fibroids","volume":"94","author":"Yang","year":"2016","journal-title":"Biol. Reprod."},{"key":"10.1016\/j.celrep.2019.11.077_bib92","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1186\/s13059-015-0668-3","article-title":"Inferring regulatory element landscapes and transcription factor networks from cancer methylomes","volume":"16","author":"Yao","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2019.11.077_bib93","doi-asserted-by":"crossref","first-page":"3197","DOI":"10.1242\/dev.128.16.3197","article-title":"Functional specificity of the Hoxa13 homeobox","volume":"128","author":"Zhao","year":"2001","journal-title":"Development"},{"key":"10.1016\/j.celrep.2019.11.077_bib94","doi-asserted-by":"crossref","first-page":"4071","DOI":"10.1093\/nar\/24.20.4071","article-title":"Genomic structure and expression of the murine Hmgi-c gene","volume":"24","author":"Zhou","year":"1996","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib95","first-page":"e22","article-title":"Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes","volume":"45","author":"Zhou","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2019.11.077_bib96","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/s41588-018-0073-4","article-title":"DNA methylation loss in late-replicating domains is linked to mitotic cell division","volume":"50","author":"Zhou","year":"2018","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2019.11.077_bib97","first-page":"e123","article-title":"SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions","volume":"46","author":"Zhou","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124719315682?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124719315682?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T10:49:53Z","timestamp":1761907793000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124719315682"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12]]},"references-count":107,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["S2211124719315682"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2019.11.077","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/452342","asserted-by":"object"}]},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2019,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2019.11.077","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2019 The Author(s).","name":"copyright","label":"Copyright"}]}}