Super-enhancers are a large cluster of transcriptionally active enhancers enriched in enhancer-associated chromatin characteristics. Compared to typical enhancers, super-enhancers are larger, exhibit higher transcription factor density, and are frequently associated with key lineage-specific genes that control cell state and differentiation in somatic cells.
Here, we developed a comprehensive human and mouse super-enhancer database (SEdb, http://www.licpathway.net/sedb) that aimed to provide a large number of available resources on human and mouse super-enhancers. The database was annotated with potential functions of super-enhancers in the TF-gene regulation. SEdb provides detailed genetic and epigenetic annotation information on super-enhancers. Information includes common SNPs, motif changes, expression quantitative trait locus (eQTL), risk SNPs, transcription factor binding sites (TFBSs), CRISPR/Cas9 target sites,DNase I hypersensitivity sites (DHSs),chromatin accessibility regions, transcriptional regulators (TRs), methylation sites, chromatin interactions regions and TADs. for in-depth analyses of super-enhancers. SEdb will help elucidate super-enhancer-related functions and find potential biological effects.
The current version of SEdb documented a total of 1,717,744 SEs from 2,670 samples including 541 original human sample, 1,198 new human samples and 931 mouse samples (more than >5 times of SEdb 1.0, which includes 331,601 SEs). These human and mouse sample are from NCBI GEO/SRA, ENCODE, Roadmap,GGR and NGDC GSA. Especially, unlike existing super-enhancer databases, we manually curated and classified over 2600 available H3K27ac samples
For more detailed statistics, please see the "Statistics" page.
SEdb-calculated super-enhancers based on H3K27ac ChIP-seq data. Genetic and epigenetic annotations were collected or calculated including common SNPs, eQTLs, risk SNPs, TFBSs, CRISPR/Cas9 target sites, DHSs, enhancers, motif changes, LD SNPs,chromatin accessibility regions, TRs, methylation sites, chromatin interactions regions and TADs. Users query super-enhancers using eight options: Species,Data sources, Biosample type, Tissue type, Biosample name, Chromosome, Start position and End position for details on super-enhancers. SEdb includes analytical tools and personalized genome browser to discover potential biological effects of super-enhancers.