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. The current version of SEdb documented a total of 331,601 super-enhancers from 542 samples. 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. 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.
Browse sample information:The ‘Data-Browse’ page is an interactive and alphanumerically sortable table that allows users to quickly search for samples and customize filters using ‘Data sources’, ‘Biosample type’, ‘Tissue type’ and ‘Biosample name’. To view super-enhancers for a given sample, users click on ‘Sample ID’.
Query super-enhancer:SEdb provides a variety of query methods, including tissue-category-based, gene-based, and sample-based advanced queries. Based on the tissue query, users can query the super-enhancer for all samples of a particular type of tissue. In the gene-based query, users can query a gene of interest and SEdb will return all super-enhancers that match the super-enhancer-gene relationship for all samples. In the sample-based advanced query, users determine the scope of the super-enhancer query by determining the sample and genome location for the results of interest.
Super-enhancer details:In addition to general information about the super-enhancer, SEdb lists more detailed annotation information including common SNPs, eQTLs, risk SNPs, TFBSs, CRISPR/Cas9 target sites, DHSs and enhancers.
Gene-SE analysis tool:Using the ‘Gene-SE analysis’ tool, users submit a gene and analyze super-enhancers associated with it via relationships between the super-enhancer and associated genes identified under different strategies (Six strategies: The closest active, ROSE overlap, ROSE proximal, ROSE closest, Lasso and PreSTIGE).
SNP-SE analysis tool:With the ‘SNP-SE analysis’ tool, users submit a common SNP and find super-enhancers in which it appears, the super-enhancer’s annotation information and LD SNPs of five super-populations.
Overlap analysis tool:With the ‘Overlap analysis’ tool, users submit a ’.bed’ file and identify super-enhancers with overlapping relationships with the submitted regions by setting the percentage of overlap.
More functions please operate
10/16/2017 Database construction
06/11/2018 The database is online
08/02/2018 Add gene-based and organization-based query capabilities
10/17/2018 SEdb is accepted by Nucleic Acids Research
02/03/2019 Delete a sample (SE_00_002), SEdb now contains 541 samples
03/13/2019 Update the download files to provide the associated genes of super-enhancer
03/14/2019 Update the page of 'Home' and 'Submit'