ArticleNucleic acids research2022
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- scRiskDB: a single-cell epigenomic resource linking complex traits to regulatory mechanisms across human tissues.Database : the journal of biological databases and curation · 2026Article
- scAED: a framework for mapping the enhancer state at single-cell resolution.Briefings in bioinformatics · 2025Article
- SemiLT: A Multianchor Transfer Learning Method for Cross-Modality Cell Label Annotation from scRNA-seq to scATAC-seq.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data.Bioinformatics (Oxford, England) · 2025Article
- Ocelli: an open-source tool for the analysis and visualization of developmental multimodal single-cell data.NAR genomics and bioinformatics · 2025Article
- scBlood: A comprehensive single-cell accessible chromatin database of blood cells.Computational and structural biotechnology journal · 2024Article
- Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.Nucleic acids research · 2024Article
- HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.Briefings in bioinformatics · 2024Article
- MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.Nucleic acids research · 2024Article
- scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species.Nucleic acids research · 2024Article
- Article
- Review
- Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences.BMC genomics · 2023Article
- ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms.Nucleic acids research · 2023Article
- The 2022 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2022Article
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Authors and funding
11 authors.
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Abstract
Previous studies on enhancers and their target genes were largely based on bulk samples that represent 'average' regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populations. 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.