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

Super-enhancer is a newly proposed concept, which refers to clusters of enhancers that can drive cell-typespecific gene expression and are crucial in cell identity. Many disease-associated sequence variations are enriched in the 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 for more than 100 cell types in human and mouse. However, no centralized resource to integrate all these findings is available yet. 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 further study of transcriptional control of cell identity and disease by archiving computationally produced data. This data can be easily send to Galaxy, GREAT and Cistrome web servers for further downstream analysis. dbSUPER provides a responsive and user-friendly web interface to facilitate efficient and comprehensive searching and browsing. dbSUPER provides downloadable and exportable features in a variety of data formats, and can be visualized in UCSC genome browser while custom tracks will be added automatically. Further, dbSUPER lists genes associated with super-enhancers and links to various databases, including GeneCards, UniProt and Entrez. Our database also provides an overlap analysis tool, to check the overlap of user defined regions with the current database. We believe, dbSUPER is a valuable resource for the bioinformatics and genetics research community. Database URL: http://bioinfo.au.tsinghua.edu.cn/dbsuper Introduction Enhancers are cis-regulatory elements of DNA that enhance the transcription of target genes by communicating with core promoter though several mechanisms including; looping, tracking, linking, and relocation models (1–6). These enhancers contain binding sites for sequence-specific transcription factors (TFs), which help to recruit coactivators and RNA polymerase II to target genes (2–5). Since the discovery of the first enhancer in animal virus SV40 (7), there has been tremendous development of technology and methodology to study the role of enhancers in gene expression. There can be thousands of active enhancers operating in a single mammalian cell, and in total there maybe ~1 million enhancers in the human genome (8, 9). Many . CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/014803 doi: bioRxiv preprint first posted online Feb. 5, 2015;