What is SEdb?
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 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. 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.
How can I use SEdb ?
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: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.
News and Updates
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 SEdb v1.01: Delete a sample (SE_00_002), SEdb now contains 541 samples
03/13/2019 SEdb v1.02: Update the download files to provide the associated genes of super-enhancer
03/14/2019 SEdb v1.03: Update the page of 'Home' and 'Submit'
10/31/2020 SEdb v1.04: Update the page of 'Home'
05/21/2021 SEdb v1.05: Update the page of 'Data-Browse' and 'Download'
Publication
Jiang Y, Qian F, Bai X, Liu Y, Wang Q, Ai B, Han X, Shi S, Zhang J, Li X, Tang Z, Pan Q, Wang Y, Wang F, Li C. SEdb: a comprehensive human super-enhancer database. Nucleic Acids Res. 2019 Jan 8;47(D1):D235-D243. doi: https://doi.org/10.1093/nar/gky1025 PMID: 30371817; PMCID: PMC6323980.
Sister Projects
ENdb
ENdb: an experimentally supported enhancer database for human and mouse
SEanalysis
SEanalysis: a web tool for super-enhancer associated regulatory analysis
LncSEA
LncSEA: a comprehensive human lncRNA sets resource and enrichment analysis platform
ATACdb
ATACdb: A comprehensive human chromatin accessibility database
KnockTF
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription
factors
TRCirc
TRCirc: a resource for transcriptional regulation information of circRNAs
TRlnc
TRlnc: a comprehensive database of human transcriptional regulation of lncRNAs
VARAdb
VARAdb: a variation annotation database for human