{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T04:09:50Z","timestamp":1793851790956,"version":"4.6.1"},"reference-count":70,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T00:00:00Z","timestamp":1699920000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["809293"],"award-info":[{"award-number":["809293"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001003","name":"Boehringer Ingelheim","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001003","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1745302"],"award-info":[{"award-number":["1745302"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["U01HG0007587"],"award-info":[{"award-number":["U01HG0007587"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["UL1 TR002535"],"award-info":[{"award-number":["UL1 TR002535"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["F32HD091966"],"award-info":[{"award-number":["F32HD091966"]}],"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":["K23HD092588"],"award-info":[{"award-number":["K23HD092588"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017743","name":"Knobloch Family Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017743","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Genomics"],"published-print":{"date-parts":[[2024,1]]},"DOI":"10.1016\/j.xgen.2023.100462","type":"journal-article","created":{"date-parts":[[2023,12,13]],"date-time":"2023-12-13T10:33:38Z","timestamp":1702463618000},"page":"100462","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":56,"title":["The human Y and inactive X chromosomes similarly modulate autosomal gene expression"],"prefix":"10.1016","volume":"4","author":[{"given":"Adrianna K.","family":"San Roman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Skaletsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander K.","family":"Godfrey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neha V.","family":"Bokil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Levi","family":"Teitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isani","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura V.","family":"Blanton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel W.","family":"Bellott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatyana","family":"Pyntikova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian","family":"Lange","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Koutseva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer F.","family":"Hughes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sidaly","family":"Phou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley","family":"Buscetta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Kruszka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Banks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amalia","family":"Dutra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evgenia","family":"Pak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia C.","family":"Lasutschinkow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colleen","family":"Keen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanlee M.","family":"Davis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela E.","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole R.","family":"Tartaglia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carole","family":"Samango-Sprouse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilian","family":"Muenke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9920-3411","authenticated-orcid":false,"given":"David C.","family":"Page","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xgen.2023.100462_bib1","series-title":"Sex Chromosomes and Sex-Linked Genes","author":"Ohno","year":"1967"},{"key":"10.1016\/j.xgen.2023.100462_bib2","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1126\/science.286.5441.964","article-title":"Four evolutionary strata on the human X chromosome","volume":"286","author":"Lahn","year":"1999","journal-title":"Science"},{"key":"10.1016\/j.xgen.2023.100462_bib3","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/190372a0","article-title":"Gene action in the X-chromosome of the mouse (Mus musculus L.)","volume":"190","author":"Lyon","year":"1961","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib4","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/349038a0","article-title":"A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome","volume":"349","author":"Brown","year":"1991","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib5","first-page":"147","article-title":"The problem of complete Y-linkage in man","volume":"9","author":"Stern","year":"1957","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib6","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1038\/nature01722","article-title":"The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes","volume":"423","author":"Skaletsky","year":"2003","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib7","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/nature03479","article-title":"X-inactivation profile reveals extensive variability in X-linked gene expression in females","volume":"434","author":"Carrel","year":"2005","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib8","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1038\/nature24265","article-title":"Landscape of X chromosome inactivation across human tissues","volume":"550","author":"Tukiainen","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib9","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1126\/science.278.5338.675","article-title":"Functional coherence of the human Y chromosome","volume":"278","author":"Lahn","year":"1997","journal-title":"Science"},{"key":"10.1016\/j.xgen.2023.100462_bib10","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/nature13206","article-title":"Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators","volume":"508","author":"Bellott","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib11","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1007\/s00439-017-1799-2","article-title":"Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men","volume":"136","author":"Forsberg","year":"2017","journal-title":"Hum. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib12","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":"10.1016\/j.xgen.2023.100462_bib13","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaw7317","article-title":"Conservation, acquisition, and functional impact of sex-biased gene expression in mammals","volume":"365","author":"Naqvi","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.xgen.2023.100462_bib14","doi-asserted-by":"crossref","DOI":"10.1126\/science.aba3066","article-title":"The impact of sex on gene expression across human tissues","volume":"369","author":"Oliva","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.xgen.2023.100462_bib15","article-title":"The human inactive X chromosome modulates expression of the active X chromosome","volume":"3","author":"San Roman","year":"2023","journal-title":"Cell Genom."},{"key":"10.1016\/j.xgen.2023.100462_bib16","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.xgen.2023.100462_bib17","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1016\/j.cell.2019.06.026","article-title":"Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility","volume":"178","author":"Guan","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.xgen.2023.100462_bib18","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.27159","article-title":"Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancer","volume":"6","author":"Cato","year":"2017","journal-title":"Elife"},{"key":"10.1016\/j.xgen.2023.100462_bib19","doi-asserted-by":"crossref","first-page":"R122","DOI":"10.1186\/gb-2013-14-11-r122","article-title":"Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome","volume":"14","author":"Cotton","year":"2013","journal-title":"Genome Biol."},{"key":"10.1016\/j.xgen.2023.100462_bib20","doi-asserted-by":"crossref","first-page":"13015","DOI":"10.1073\/pnas.1806811115","article-title":"Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts","volume":"115","author":"Garieri","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xgen.2023.100462_bib21","doi-asserted-by":"crossref","first-page":"1629","DOI":"10.1101\/gr.275677.121","article-title":"Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases","volume":"31","author":"Sauteraud","year":"2021","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2023.100462_bib22","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s13293-015-0053-7","article-title":"Derivation of consensus inactivation status for X-linked genes from genome-wide studies","volume":"6","author":"Balaton","year":"2015","journal-title":"Biol. Sex Differ."},{"key":"10.1016\/j.xgen.2023.100462_bib23","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1146\/annurev-cellbio-101011-155807","article-title":"New Insights into the Troubles of Aneuploidy","volume":"28","author":"Siegel","year":"2012","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"10.1016\/j.xgen.2023.100462_bib24","doi-asserted-by":"crossref","first-page":"15826","DOI":"10.1073\/pnas.1010383107","article-title":"Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict","volume":"107","author":"Lemos","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xgen.2023.100462_bib25","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1038\/ng1754","article-title":"High mutation rates have driven extensive structural polymorphism among human Y chromosomes","volume":"38","author":"Repping","year":"2006","journal-title":"Nat. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib26","first-page":"68","article-title":"The 1000 Genomes Project Consortium (2015). A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib27","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nature12531","article-title":"Transcriptome and genome sequencing uncovers functional variation in humans","volume":"501","author":"Lappalainen","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2023.100462_bib28","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/ng0794-414","article-title":"Highly homologous loci on the X and Y chromosomes are hot-spots for ectopic recombinations leading to XX maleness","volume":"7","author":"Weil","year":"1994","journal-title":"Nat. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib29","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1016\/0092-8674(89)90061-5","article-title":"ZFX has a gene structure similar to ZFY, the putative human sex determinant, and escapes X inactivation","volume":"57","author":"Schneider-G\u00e4dicke","year":"1989","journal-title":"Cell"},{"key":"10.1016\/j.xgen.2023.100462_bib30","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1073\/pnas.87.5.1681","article-title":"Comparison of human ZFY and ZFX transcripts","volume":"87","author":"Palmer","year":"1990","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xgen.2023.100462_bib31","doi-asserted-by":"crossref","first-page":"5986","DOI":"10.1093\/nar\/gkaa384","article-title":"Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters","volume":"48","author":"Ni","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xgen.2023.100462_bib32","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1101\/gr.228809.117","article-title":"ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters","volume":"28","author":"Rhie","year":"2018","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2023.100462_bib33","doi-asserted-by":"crossref","first-page":"2631","DOI":"10.1093\/hmg\/dds088","article-title":"Human and mouse ZFY genes produce a conserved testis-specific transcript encoding a zinc finger protein with a short acidic domain and modified transactivation potential","volume":"21","author":"Decarpentrie","year":"2012","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib34","first-page":"681","article-title":"Mouse Zfx protein is similar to Zfy-2: each contains an acidic activating domain and 13 zinc fingers","volume":"10","author":"Mardon","year":"1990","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.xgen.2023.100462_bib35","doi-asserted-by":"crossref","DOI":"10.3390\/ijms17101737","article-title":"Zinc Finger and X-Linked Factor (ZFX) Binds to Human SET Transcript 2 Promoter and Transactivates SET Expression","volume":"17","author":"Xu","year":"2016","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.xgen.2023.100462_bib36","doi-asserted-by":"crossref","first-page":"7398","DOI":"10.1073\/pnas.1802889115","article-title":"Sex-chromosome dosage effects on gene expression in humans","volume":"115","author":"Raznahan","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xgen.2023.100462_bib37","doi-asserted-by":"crossref","first-page":"4864","DOI":"10.1073\/pnas.1910003117","article-title":"Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage","volume":"117","author":"Zhang","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xgen.2023.100462_bib38","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms15403","article-title":"Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression","volume":"8","author":"Rosenbluh","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xgen.2023.100462_bib39","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s12915-017-0352-z","article-title":"The landscape of sex-differential transcriptome and its consequent selection in human adults","volume":"15","author":"Gershoni","year":"2017","journal-title":"BMC Biol."},{"key":"10.1016\/j.xgen.2023.100462_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107795","article-title":"Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues","volume":"31","author":"Lopes-Ramos","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.xgen.2023.100462_bib41","doi-asserted-by":"crossref","DOI":"10.1038\/srep34220","article-title":"Widespread DNA hypomethylation and differential gene expression in Turner syndrome","volume":"6","author":"Trolle","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.xgen.2023.100462_bib42","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/ajmg.c.31799","article-title":"Epigenetic and transcriptomic consequences of excess X-chromosome material in 47,XXX syndrome-A comparison with Turner syndrome and 46,XX females","volume":"184","author":"Nielsen","year":"2020","journal-title":"Am. J. Med. Genet. C Semin. Med. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib43","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13073-023-01169-4","article-title":"X chromosome dosage and the genetic impact across human tissues","volume":"15","author":"Viuff","year":"2023","journal-title":"Genome Med."},{"key":"10.1016\/j.xgen.2023.100462_bib44","article-title":"Aneuploidy effects on human gene expression across three cell types","volume":"120","author":"Liu","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xgen.2023.100462_bib45","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1146\/annurev-genet-112414-055311","article-title":"The Biology and Evolution of Mammalian Y Chromosomes","volume":"49","author":"Hughes","year":"2015","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib46","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1101\/gr.268516.120","article-title":"Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals","volume":"31","author":"Bellott","year":"2021","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2023.100462_bib47","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1101\/gr.261248.120","article-title":"Quantitative analysis of Y-Chromosome gene expression across 36 human tissues","volume":"30","author":"Godfrey","year":"2020","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2023.100462_bib53","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.xgen.2023.100462_bib54","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xgen.2023.100462_bib68","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.19760","article-title":"Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation","volume":"5","author":"Horlbeck","year":"2016","journal-title":"Elife"},{"key":"10.1016\/j.xgen.2023.100462_bib69","doi-asserted-by":"crossref","first-page":"2564","DOI":"10.1158\/0008-5472.CAN-18-2674","article-title":"Genome-Wide Interrogation of Human Cancers Identifies EGLN1 Dependency in Clear Cell Ovarian Cancers","volume":"79","author":"Price","year":"2019","journal-title":"Cancer Res."},{"key":"10.1016\/j.xgen.2023.100462_bib49","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xgen.2023.100462_bib51","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xgen.2023.100462_bib52","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":"10.1016\/j.xgen.2023.100462_bib64","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.xgen.2023.100462_bib63","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.xgen.2023.100462_bib61","doi-asserted-by":"crossref","first-page":"W566","DOI":"10.1093\/nar\/gkv468","article-title":"ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap","volume":"43","author":"Metsalu","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xgen.2023.100462_bib48","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1101\/gr.080531.108","article-title":"The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes","volume":"19","author":"Pruitt","year":"2009","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2023.100462_bib50","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.1","article-title":"Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences","volume":"4","author":"Soneson","year":"2015","journal-title":"F1000Res."},{"key":"10.1016\/j.xgen.2023.100462_bib55","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.ajhg.2018.07.007","article-title":"Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages","volume":"103","author":"Teitz","year":"2018","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib56","doi-asserted-by":"crossref","first-page":"e105","DOI":"10.1093\/nar\/gkn425","article-title":"Substantial biases in ultra-short read data sets from high-throughput DNA sequencing","volume":"36","author":"Dohm","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xgen.2023.100462_bib57","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1038\/nbt.2702","article-title":"Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories","volume":"31","author":"'t Hoen","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xgen.2023.100462_bib58","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/j.cell.2009.07.042","article-title":"Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes","volume":"138","author":"Lange","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.xgen.2023.100462_bib59","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.ygeno.2013.04.018","article-title":"Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms","volume":"102","author":"Lange","year":"2013","journal-title":"Genomics"},{"key":"10.1016\/j.xgen.2023.100462_bib60","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xgen.2023.100462_bib62","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1093\/hmg\/6.11.1985","article-title":"Abnormal XY interchange between a novel isolated protein kinase gene, PRKY, and its homologue, PRKX, accounts for one third of all (Y+)XX males and (Y-)XY females","volume":"6","author":"Schiebel","year":"1997","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.xgen.2023.100462_bib65","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1016\/j.cell.2013.12.001","article-title":"Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR\/Cas System","volume":"155","author":"Chen","year":"2013","journal-title":"Cell"},{"key":"10.1016\/j.xgen.2023.100462_bib66","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1126\/science.aag2445","article-title":"Systematic mapping of functional enhancer\u2013promoter connections with CRISPR interference","volume":"354","author":"Fulco","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.xgen.2023.100462_bib67","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1261\/rna.2192803","article-title":"Lentivirus-delivered stable gene silencing by RNAi in primary cells","volume":"9","author":"Stewart","year":"2003","journal-title":"RNA"},{"key":"10.1016\/j.xgen.2023.100462_bib70","series-title":"R: A Language and Environment for Statistical Computing","year":"2020"}],"container-title":["Cell Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666979X23003063?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666979X23003063?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T07:28:04Z","timestamp":1763018884000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666979X23003063"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1]]},"references-count":70,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1]]}},"alternative-id":["S2666979X23003063"],"URL":"https:\/\/doi.org\/10.1016\/j.xgen.2023.100462","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.06.05.543763","asserted-by":"object"}]},"ISSN":["2666-979X"],"issn-type":[{"value":"2666-979X","type":"print"}],"subject":[],"published":{"date-parts":[[2024,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"The human Y and inactive X chromosomes similarly modulate autosomal gene expression","name":"articletitle","label":"Article Title"},{"value":"Cell Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xgen.2023.100462","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors.","name":"copyright","label":"Copyright"}],"article-number":"100462"}}