{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T09:16:28Z","timestamp":1772961388928,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,9]],"date-time":"2021-11-09T00:00:00Z","timestamp":1636416000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Provence-Alpes-C\u00f4te d\u2019Azur Regional Council"},{"DOI":"10.13039\/501100001677","name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004562","name":"French Ministry of Higher Education and Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004562","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007586","name":"Aix-Marseille Universit\u00e9","doi-asserted-by":"publisher","award":["ANR-10-EQPX-29-01"],"award-info":[{"award-number":["ANR-10-EQPX-29-01"]}],"id":[{"id":"10.13039\/100007586","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Institute MarMaRa","award":["AMX-19-IET- 007"],"award-info":[{"award-number":["AMX-19-IET- 007"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>ReMap (https:\/\/remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed\u00a0&amp;gt;11 000 DNA-binding sequencing datasets from public sources across four species. The updated Human regulatory atlas includes 8103 datasets covering a total of 1210 transcriptional regulators (TRs) with a catalog of 182 million (M) peaks, while the updated Arabidopsis atlas reaches 4.8M peaks, 423 TRs across 694 datasets. Also, this ReMap release is enriched by two new regulatory catalogs for Mus musculus and Drosophila melanogaster. First, the Mouse regulatory catalog consists of 123M peaks across 648 TRs as a result of the integration and validation of 5503 ChIP-seq datasets. Second, the Drosophila melanogaster catalog contains 16.6M peaks across 550 TRs from the integration of 1205 datasets. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers. Finally, ReMap 2022 comes with a new Cis Regulatory Module identification method, improved quality controls, faster search results, and better user experience with an interactive tour and video tutorials on browsing and filtering ReMap catalogs.<\/jats:p>","DOI":"10.1093\/nar\/gkab996","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T20:54:10Z","timestamp":1634158450000},"page":"D316-D325","source":"Crossref","is-referenced-by-count":429,"title":["ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7612-4953","authenticated-orcid":false,"given":"Fayrouz","family":"Hammal","sequence":"first","affiliation":[{"name":"Aix Marseille Univ, INSERM, TAGC, Marseille, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6119-2438","authenticated-orcid":false,"given":"Pierre","family":"de\u00a0Langen","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, TAGC, Marseille, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1518-4562","authenticated-orcid":false,"given":"Aur\u00e9lie","family":"Bergon","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, TAGC, Marseille, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2401-0292","authenticated-orcid":false,"given":"Fabrice","family":"Lopez","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, TAGC, Marseille, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0834-7135","authenticated-orcid":false,"given":"Benoit","family":"Ballester","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, TAGC, Marseille, France"}]}],"member":"286","published-online":{"date-parts":[[2021,11,9]]},"reference":[{"key":"2022010507415548700_B1","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"Johnson","year":"2007","journal-title":"Science"},{"key":"2022010507415548700_B2","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2013update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2022010507415548700_B3","doi-asserted-by":"crossref","first-page":"D1502","DOI":"10.1093\/nar\/gkaa1062","article-title":"From ArrayExpress to BioStudies","volume":"49","author":"Sarkans","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507415548700_B4","doi-asserted-by":"crossref","first-page":"D71","DOI":"10.1093\/nar\/gkaa982","article-title":"DDBJ update: streamlining submission and access of human data","volume":"49","author":"Fukuda","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507415548700_B5","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.cell.2018.01.029","article-title":"The human transcription factors","volume":"172","author":"Lambert","year":"2018","journal-title":"Cell"},{"key":"2022010507415548700_B6","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/nrg2538","article-title":"A census of human transcription factors: function, expression and evolution","volume":"10","author":"Vaquerizas","year":"2009","journal-title":"Nat. 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