Super-enhancers are important for controlling and defining the expression of cell-specific genes. With research on human disease and biological processes, human H3K27ac ChIP-seq datasets are accumulating rapidly, creating the urgent need to collect and process these data comprehensively and efficiently. More importantly, many studies showed that super-enhancer-associated single nucleotide polymorphisms (SNPs) and transcription factors (TFs) strongly influence human disease and biological processes.
Here, we developed a comprehensive human super-enhancer database (SEdb, http://www.licpathway.net/sedb) that aimed to provide a large number of available resources on human super-enhancers. The database was annotated with potential functions of super-enhancers in the gene regulation. Furthermore, 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 and Dnase I hypersensitivity sites (DHSs) 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 331 601 Super-enhancers and 1 992 738 Super-enhancer elements over 540 samples, including the samples from NCBI GEO/SRA, ENCODE, Roadmap and GGR. Especially, unlike existing super-enhancer databases, we manually curated and classified 410 available H3K27ac samples from more than 2,000 ChIP-seq samples from NCBI GEO/SRA. For all samples, super-enhancers were identified by using a unified system environment and software parameters.
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 and LD SNPs. Users query super-enhancers using seven options: 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.