Super-enhancers are genome regions that are large clusters of transcriptional enhancers. The term ‘super-enhancer’ was used for the first time by Chen et al. in 2004. Super-enhancers differ from typical enhancers in size, transcription factor density and content, and the ability to activate transcription.
Provides a collection of super-enhancers. dbSUPER offers functions to send data to Galaxy instances, GREAT and Cistrome web-servers for downstream analysis. It lists genes associated with super-enhancers and also links to external databases such as GeneCards, UniProt and Entrez. This database furnishes an overlap analysis tool to annotate user-defined regions. It is useful for studies related to transcriptional control of cell identity and disease.
Gathers a large number of available resources on human super-enhancers. SEdb enables the annotation of potential cell specific functions in gene regulation. It contains genetic and epigenetic information about super-enhancers including common single nucleotide polymorphisms (SNPs), motif changes, expression quantitative trait loci (eQTLs), risk SNPs, transcription factor binding sites (TFBSs), CRISPR/Cas9 target sites, Dnase I hypersensitivity sites (DHSs) and enhancers.
Stores core transcription regulatory circuitry (CRC) models human and 50 murine cell line/tissue samples. dbCoRC is a comprehensive and interactive database that provides a platform to store, search, visualize, and analyze CRCs. The database is developed on H3K27ac ChIP-seq data. It provides a resource to fulfill the fast expanding scientific exploration of transcriptional control and regulatory circuitries in normal and disease conditions.
Focuses on integrating experimentally and computationally identified super-enhancers and annotating their potential roles in the regulation of cell identity gene expression in a cell type-specific manner. The current release of SEA incorporates 83 996 super-enhancers computationally or experimentally identified in 134 cell types/tissues/diseases, including human (75 439, three of which were experimentally identified), mouse (5879, five of which were experimentally identified), Drosophila melanogaster (1774) and Caenorhabditis elegans (904). To facilitate data extraction, SEA supports multiple search options, including species, genome location, gene name, cell type/tissue and super-enhancer name. The response provides detailed (epi)genetic information, incorporating cell type specificity, nearby genes, transcriptional factor binding sites, CRISPR/Cas9 target sites, evolutionary conservation, SNPs, H3K27ac, DNA methylation, gene expression and TF ChIP-seq data. Moreover, analytical tools and a genome browser were developed for users to explore super-enhancers and their roles in defining cell identity and disease processes in depth.