{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T22:57:59Z","timestamp":1779922679144,"version":"3.53.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,10,26]],"date-time":"2018-10-26T00:00:00Z","timestamp":1540512000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Cedars-Sinai\u2019s Samuel Oschin Comprehensive Cancer Institute"},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation","doi-asserted-by":"publisher","award":["2016\/01389-7"],"award-info":[{"award-number":["2016\/01389-7"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation","doi-asserted-by":"publisher","award":["2015\/07925-5"],"award-info":[{"award-number":["2015\/07925-5"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NIH\/NCI Informatics Technology for Cancer Research","award":["1U01CA184826"],"award-info":[{"award-number":["1U01CA184826"]}]},{"name":"Genomic Data Analysis Network","award":["1U24CA210969"],"award-info":[{"award-number":["1U24CA210969"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01CA190182"],"award-info":[{"award-number":["R01CA190182"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>DNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R\/Bioconductor package ELMER (Enhancer Linking by Methylation\/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use pre-defined sample groupings. We show that Supervised mode significantly increases statistical power and identifies additional GRNs and associated Master Regulators, such as SOX11 and KLF5 in Basal-like breast cancer.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ELMER v.2 is available as an R\/Bioconductor package at http:\/\/bioconductor.org\/packages\/ELMER\/.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty902","type":"journal-article","created":{"date-parts":[[2018,10,25]],"date-time":"2018-10-25T07:14:48Z","timestamp":1540451688000},"page":"1974-1977","source":"Crossref","is-referenced-by-count":109,"title":["ELMER v.2: an R\/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles"],"prefix":"10.1093","volume":"35","author":[{"given":"Tiago C","family":"Silva","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"},{"name":"Department of Genetics, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon G","family":"Coetzee","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Gull","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijing","family":"Yao","sequence":"additional","affiliation":[{"name":"Bioinformatics Research & Early Development, Roche Sequencing Solutions, Belmont, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis J","family":"Hazelett","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Houtan","family":"Noushmehr","sequence":"additional","affiliation":[{"name":"Department of Genetics, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil"},{"name":"Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"De-Chen","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin P","family":"Berman","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA"},{"name":"Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,10,26]]},"reference":[{"key":"2023012713231523800_bty902-B1","doi-asserted-by":"crossref","first-page":"R21","DOI":"10.1186\/gb-2013-14-3-r21","article-title":"Dna methylation of distal regulatory sites characterizes dysregulation of cancer genes","volume":"14","author":"Aran","year":"2013","journal-title":"Genome Biol."},{"key":"2023012713231523800_bty902-B2","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.cell.2013.06.018","article-title":"DNA methylation of transcriptional enhancers and cancer predisposition","volume":"154","author":"Aran","year":"2013","journal-title":"Cell"},{"key":"2023012713231523800_bty902-B3","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/ng.127","article-title":"An embryonic stem cell\u2013like gene expression signature in poorly differentiated aggressive human tumors","volume":"40","author":"Ben-Porath","year":"2008","journal-title":"Nat. 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