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In recent years, single-cell sequencing technology has enabled the profiling of open chromatin accessibility at the single-cell level (scATAC-seq), which can be used to annotate the enhancers and promoters in specific cell types. A comprehensive resource is highly desirable for exploring how the enhancers regulate the target genes at the single-cell level. Hence, we designed a single-cell database scEnhancer (http:\/\/enhanceratlas.net\/scenhancer\/), covering 14 527 776 enhancers and 63 658 600 enhancer-gene interactions from 1 196 906 single cells across 775 tissue\/cell types in three species. An unsupervised learning method was employed to sort and combine tens or hundreds of single cells in each tissue\/cell type to obtain the consensus enhancers. In addition, we utilized a cis-regulatory network algorithm to identify the enhancer-gene connections. Finally, we provided a user-friendly platform with seven useful modules to search, visualize, and browse the enhancers\/genes. This database will facilitate the research community towards a functional analysis of enhancers at the single-cell level.<\/jats:p>","DOI":"10.1093\/nar\/gkab1032","type":"journal-article","created":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T13:48:11Z","timestamp":1634651291000},"page":"D371-D379","source":"Crossref","is-referenced-by-count":25,"title":["scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue\/cell types in three species"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0466-9081","authenticated-orcid":false,"given":"Tianshun","family":"Gao","sequence":"first","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"},{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zilong","family":"Zheng","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yihang","family":"Pan","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"},{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengming","family":"Zhu","sequence":"additional","affiliation":[{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. 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China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuo","family":"Fang","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"},{"name":"Department of Oncology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nan","family":"Wang","sequence":"additional","affiliation":[{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Zhou","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. 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