ArticleNucleic acids research2020
SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Conserved enhancer association of piRNAs and the implication in germ cell fate surveillance.Genome biology · 2026Article
- Understanding super enhancers in genome architecture and their roles in livestock breeding.BMC genomics · 2026Review
- Crosstalk BetweenCancers · 2026Review
- ePerturbDB: enhancer's experimental perturbation database.Database : the journal of biological databases and curation · 2026Article
- scVMAP: a comprehensive platform for integrating single-cell chromatin accessibility regions with causal variants.Nucleic acids research · 2026Article
- SEdb 3.0: a comprehensive super-enhancer database across multiple species.Nucleic acids research · 2026Article
- CircleBase V2: an eccDNA annotation platform across cancers and species.Nucleic acids research · 2026Article
- SEA version 4.0: a major expansion and update of the Super-Enhancer Archive.Nucleic acids research · 2026Article
- Chromatin Accessibility Profiling of Keratinocytes from Clinically Healed Psoriatic Skin Reveals Epigenetic Alterations.JID innovations : skin science from molecules to population health · 2026Article
- Interlocking host and viral cis-regulatory networks drive Merkel cell carcinoma.The Journal of clinical investigation · 2025Article
- Decoding cancer heterogeneity through super-enhancer landscapes: from subtype discovery to therapeutic opportunity.Briefings in bioinformatics · 2025Review
- Unraveling the Carcinogenic Mechanisms of Food Contaminants: An Integrated in Silico Framework Combining Network Toxicology, Machine Learning, and Molecular Docking.Journal of food science · 2025Article
- scPOEM: robust co-embedding of peaks and genes revealing peak-gene regulation.Bioinformatics (Oxford, England) · 2025Article
- Apigenin mitigates intestinal barrier dysfunction in sepsis by modulating the AKT signaling pathway.BMC gastroenterology · 2025Article
- dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data.Bioinformatics (Oxford, England) · 2025Article
- HemaCisDB: An Interactive Database for Analyzing Cis-regulatory Elements Across Hematopoietic Malignancies.Genomics, proteomics & bioinformatics · 2025Article
- SEgene identifies links between super enhancers and gene expression across cell types.NPJ systems biology and applications · 2025Article
- Transcription Factor-Wide Association Studies to Identify Functional SNPs in Alzheimer's Disease.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Mechanism investigation of Forsythoside A against esophageal squamous cell carcinomaCancer biology & therapy · 2024Article
- ABCA1-Super Enhancer RNA Promotes Cholesterol Efflux, Reduces Macrophage-Mediated Inflammation and Atherosclerosis.JACC. Basic to translational science · 2024Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Super-enhancers (SEs) are critical for the transcriptional regulation of gene expression. We developed the super-enhancer archive version 3.0 (SEA v. 3.0, http://sea.edbc.org) to extend SE research. SEA v. 3.0 provides the most comprehensive archive to date, consisting of 164 545 super-enhancers. Of these, 80 549 are newly identified from 266 cell types/tissues/diseases using an optimized computational strategy, and 52 have been experimentally confirmed with manually curated references. We now support super-enhancers in 11 species including 7 new species (zebrafish, chicken, chimp, rhesus, sheep, Xenopus tropicalis and stickleback). To facilitate super-enhancer functional analysis, we added several new regulatory datasets including 3 361 785 typical enhancers, chromatin interactions, SNPs, transcription factor binding sites and SpCas9 target sites. We also updated or developed new criteria query, genome visualization and analysis tools for the archive. This includes a tool based on Shannon Entropy to evaluate SE cell type specificity, a new genome browser that enables the visualization of SE spatial interactions based on Hi-C data, and an enhanced enrichment analysis interface that provides online enrichment analyses of SE related genes. SEA v. 3.0 provides a comprehensive database of all available SE information across multiple species, and will facilitate super-enhancer research, especially as related to development and disease.
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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.