{"doi":"10.1093/nar/gkaa382","title":"EpiRegio: analysis and retrieval of regulatory elements linked to genes","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’s activity and its estimated cell type-specific contribution to its target gene’s 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>","journal":"Nucleic Acids Research","year":2020,"id":33519,"datarank":0.8234445588094257,"base_score":3.58351893845611,"endowment":3.58351893845611,"self_citation_contribution":0.5375278407684165,"citation_network_contribution":0.2859167180410091,"self_endowment_contribution":0.5375278407684165,"citer_contribution":0.2859167180410091,"corpus_percentile":null,"corpus_rank":null,"citation_count":35,"citer_count":11,"citers_with_citation_signal":8,"citers_with_endowment":8,"datacite_reuse_total":20,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":52373,"name":"Dennis Hecker","orcid":"0000-0003-0272-243X","position":1,"is_corresponding":false},{"id":175211,"name":"Sivarajan Karunanithi","orcid":"0000-0001-6128-5351","position":2,"is_corresponding":false},{"id":68296,"name":"Florian Schmidt","orcid":"0000-0002-6362-211X","position":3,"is_corresponding":false},{"id":15023,"name":"Markus List","orcid":"0000-0002-0941-4168","position":4,"is_corresponding":false},{"id":52374,"name":"Marcel H. Schulz","orcid":"0000-0002-1252-3656","position":5,"is_corresponding":false},{"id":175210,"name":"Nina Baumgarten","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.58351893845611,"endowment":3.58351893845611,"datacite_reuse_total":20,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"32459338","pmcid":"PMC7319550","openalex_id":"https://openalex.org/W3031027624","authors":[],"funders":[{"funder_name":"Deutsches Zentrum für Herz-Kreislaufforschung","grant_id":"81Z0200101","title":null},{"funder_name":"Deutsche Forschungsgemeinschaft","grant_id":"DFG SFB/TRR 267","title":null},{"funder_name":"Deutsche Forschungsgemeinschaft","grant_id":"unidentified","title":"unidentified"}],"total_grants":3,"fwci":3.7509,"citation_percentile":0.94445693,"influential_citations":1,"citation_trend":[{"year":2019,"count":1},{"year":2020,"count":3},{"year":2021,"count":8},{"year":2022,"count":8},{"year":2023,"count":12},{"year":2024,"count":2},{"year":2025,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/48/W1/W193/33433154/gkaa382.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/48/W1/W193/33433154/gkaa382.pdf","host_type":"GOLD"},{"url":"https://academic.oup.com/nar/article-pdf/48/W1/W193/33433154/gkaa382.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/48/W1/W193/33433154/gkaa382.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkaa382","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/32459338","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7319550","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC7319550","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC7319550?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.7490/f1000research.1118243.1","host_type":""},{"url":"https://dx.doi.org/10.7490/f1000research.1118243.1","host_type":""},{"url":"https://dx.doi.org/10.5281/zenodo.3752510","host_type":""},{"url":"https://zenodo.org/records/3752510","host_type":""},{"url":"http://dx.doi.org/10.5281/zenodo.3752510","host_type":""},{"url":"https://dx.doi.org/10.5281/zenodo.3750930","host_type":""},{"url":"https://zenodo.org/records/3750930","host_type":""},{"url":"http://dx.doi.org/10.5281/zenodo.3750930","host_type":""},{"url":"https://dx.doi.org/10.5281/zenodo.3750929","host_type":""},{"url":"https://dx.doi.org/10.5281/zenodo.3758494","host_type":""},{"url":"http://dx.doi.org/10.5281/zenodo.3758494","host_type":""},{"url":"https://zenodo.org/records/3758494","host_type":""},{"url":"http://dx.doi.org/10.1093/nar/gkaa382","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gkaa382","host_type":""}],"fields_of_study":["Genomics and Chromatin Dynamics","Epigenetics and DNA Methylation","Gene expression and cancer classification","Computer Science","Biology","Medicine","0301 basic medicine","0303 health sciences","03 medical and health sciences","Chromatin Immunoprecipitation Sequencing","Disease","Gene Expression Regulation","Humans","Regulatory Elements, Transcriptional","Software","Transcription Factors"],"mesh_terms":["Chromatin Immunoprecipitation Sequencing","Disease","Gene Expression Regulation","Humans","Software","Transcription Factors","Regulatory Elements, Transcriptional"],"keywords":["Biology","Epigenomics","Gene","Regulatory sequence","Genetics","Computational biology","Chromatin","Genomics","Functional genomics","Regulation of gene expression","Genome","Gene expression","DNA methylation","web server","enhancer target association","Gene Expression Regulation","Web Server Issue","Chromatin Immunoprecipitation Sequencing","Humans","Disease","Regulatory Elements, Transcriptional","enhancer","gene 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