Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jan 4;44(D1):D164-71.
doi: 10.1093/nar/gkv1002. Epub 2015 Oct 4.

dbSUPER: a database of super-enhancers in mouse and human genome

Aziz Khan  1 , Xuegong Zhang  2
Affiliations

dbSUPER: a database of super-enhancers in mouse and human genome

Aziz Khan et al. Nucleic Acids Res. .

Abstract

Super-enhancers are clusters of transcriptional enhancers that drive cell-type-specific gene expression and are crucial to cell identity. Many disease-associated sequence variations are enriched in super-enhancer regions of disease-relevant cell types. Thus, super-enhancers can be used as potential biomarkers for disease diagnosis and therapeutics. Current studies have identified super-enhancers in more than 100 cell types and demonstrated their functional importance. However, a centralized resource to integrate all these findings is not currently available. We developed dbSUPER (http://bioinfo.au.tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further studies related to transcriptional control of cell identity and disease. dbSUPER provides a responsive and user-friendly web interface to facilitate efficient and comprehensive search and browsing. The data can be easily sent to Galaxy instances, GREAT and Cistrome web-servers for downstream analysis, and can also be visualized in the UCSC genome browser where custom tracks can be added automatically. The data can be downloaded and exported in variety of formats. Furthermore, dbSUPER lists genes associated with super-enhancers and also links to external databases such as GeneCards, UniProt and Entrez. dbSUPER also provides an overlap analysis tool to annotate user-defined regions. We believe dbSUPER is a valuable resource for the biology and genetic research communities.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Overview of super-enhancer identification, data integration, and dbSUPER workflow and features.
Figure 2.
Figure 2.
Interactive searching and browsing activity of dbSUPER. (A) Quick search feature on the homepage. (B) Browse database for mESC cell-type. (C) Results for browse database and also for quick search using keyword ‘mouse embryonic stem cell’. (D) Detailed search page, look for Sox2 gene in mESC. (E) Results of detailed search query.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Levine M., Cattoglio C., Tjian R. Looping back to leap forward: transcription enters a new era. Cell. 2014;157:13–25. - PMC - PubMed
    1. Shlyueva D., Stampfel G., Stark A. Transcriptional enhancers: from properties to genome-wide predictions. Nat. Rev. Genet. 2014;15:272–286. - PubMed
    1. Wamstad J.A., Wang X., Demuren O.O., Boyer L.A. Distal enhancers: new insights into heart development and disease. Trends Cell Biol. 2013;24:294–302. - PubMed
    1. Kolovos P., Knoch T.A., Grosveld F.G., Cook P.R., Papantonis A. Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin. 2012;5:1. - PMC - PubMed
    1. Pennacchio L.A., Bickmore W., Dean A., Nobrega M.A., Bejerano G. Enhancers: five essential questions. Nat. Rev. Genet. 2013;14:288–295. - PMC - PubMed

Publication types