{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:12:28Z","timestamp":1778058748638,"version":"3.51.4"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T00:00:00Z","timestamp":1590537600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010447","name":"Deutsches Zentrum f\u00fcr Herz-Kreislaufforschung","doi-asserted-by":"publisher","award":["81Z0200101"],"award-info":[{"award-number":["81Z0200101"]}],"id":[{"id":"10.13039\/100010447","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["DFG SFB\/TRR 267"],"award-info":[{"award-number":["DFG SFB\/TRR 267"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding regions, but their mechanisms of gene regulation are often unknown. An additional challenge is to reliably identify the target genes of the regulatory regions, which is an essential step in understanding their impact on gene expression. Here we present the EpiRegio web server, a resource of regulatory elements (REMs). REMs are genomic regions that exhibit variations in their chromatin accessibility profile associated with changes in expression of their target genes. EpiRegio incorporates both epigenomic and gene expression data for various human primary cell types and tissues, providing an integrated view of REMs in the genome. Our web server allows the analysis of genes and their associated REMs, including the REM\u2019s activity and its estimated cell type-specific contribution to its target gene\u2019s expression. Further, it is possible to explore genomic regions for their regulatory potential, investigate overlapping REMs and by that the dissection of regions of large epigenomic complexity. EpiRegio allows programmatic access through a REST API and is freely available at https:\/\/epiregio.de\/.<\/jats:p>","DOI":"10.1093\/nar\/gkaa382","type":"journal-article","created":{"date-parts":[[2020,5,4]],"date-time":"2020-05-04T12:11:50Z","timestamp":1588594310000},"page":"W193-W199","source":"Crossref","is-referenced-by-count":29,"title":["EpiRegio: analysis and retrieval of regulatory elements linked to genes"],"prefix":"10.1093","volume":"48","author":[{"given":"Nina","family":"Baumgarten","sequence":"first","affiliation":[{"name":"Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany"},{"name":"Cardio-Pulmonary Institute, Goethe University Hospital, 60590\u00a0Frankfurt am Main, Germany"},{"name":"German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany"},{"name":"Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbr\u00fccken,\u00a0Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dennis","family":"Hecker","sequence":"first","affiliation":[{"name":"Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany"},{"name":"Cardio-Pulmonary Institute, Goethe University Hospital, 60590\u00a0Frankfurt am Main, Germany"},{"name":"German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6128-5351","authenticated-orcid":false,"given":"Sivarajan","family":"Karunanithi","sequence":"first","affiliation":[{"name":"Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany"},{"name":"Cardio-Pulmonary Institute, Goethe University Hospital, 60590\u00a0Frankfurt am Main, Germany"},{"name":"German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9222-6207","authenticated-orcid":false,"given":"Florian","family":"Schmidt","sequence":"first","affiliation":[{"name":"German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany"},{"name":"Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbr\u00fccken,\u00a0Germany"},{"name":"Genome Institute of Singapore, 60 Biopolis Street, Genome, 02-01, 138672,\u00a0Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0941-4168","authenticated-orcid":false,"given":"Markus","family":"List","sequence":"first","affiliation":[{"name":"Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1252-3656","authenticated-orcid":false,"given":"Marcel H","family":"Schulz","sequence":"first","affiliation":[{"name":"Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany"},{"name":"Cardio-Pulmonary Institute, Goethe University Hospital, 60590\u00a0Frankfurt am Main, Germany"},{"name":"German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany"},{"name":"Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbr\u00fccken,\u00a0Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,27]]},"reference":[{"key":"2020062614045995200_B1","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1126\/science.281.5373.60","article-title":"Going the distance: a current view of enhancer action","volume":"281","author":"Blackwood","year":"1998","journal-title":"Science"},{"key":"2020062614045995200_B2","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1016\/j.cell.2012.04.040","article-title":"Circuitry and dynamics of human transcription factor regulatory networks","volume":"150","author":"Neph","year":"2012","journal-title":"Cell"},{"key":"2020062614045995200_B3","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/nrm3949","article-title":"The selection and function of cell type-specific enhancers","volume":"16","author":"Heinz","year":"2015","journal-title":"Nat. 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