Abstract
High-throughput reporter assays have been recently developed to directly and quantitatively assess enhancer activity for thousands of regulatory elements. However, there is still no database to collect these enhancers. We developed RAEdb, the first database to collect enhancers identified by high-throughput reporter assays. RAEdb includes 538 320 enhancers derived from eight studies, most of which were from six human cell lines. An activity score was assigned to each enhancer based on reporter assays. Based on these enhancers, 7658 epromoters (promoters with enhancer activity) were identified and stored in the database. RAEdb provides two ways of searches: the first is to search studies by species and cell line; the other is to search enhancers or epromoters by position, activity score, sequence and gene. RAEdb also provides a genome browser to query, visualize and compare enhancers. All data in RAEdb is freely available for download.
Highlights
The enhancer is a short (50∼1500 bps) region of DNA sequence that recruits transcription factors to regulate the transcription of target genes in a cell-type-specific manner [1]
RAEdb contains 538 320 enhancers derived from eight studies; 55 415 and 482 905 of these enhancers were derived from data generated by STARR-seq and MPRA method (Figure 2A and B), respectively
All the enhancers generated by STARR-seq belong to four human cell lines
Summary
The enhancer is a short (50∼1500 bps) region of DNA sequence that recruits transcription factors to regulate the transcription of target genes in a cell-type-specific manner [1]. Enhancers play a central role in regulating a wide range of important biological functions and processes, such as embryogenesis, development and homeostasis [1,2,3]. They were reported to be associated with many human complex diseases [4]. There are several databases collecting enhancers, including EnhancerAtlas [5], VISTA Enhancer Most enhancers in previous databases lack of quantitative activity scores [11, 12], which hinders computational modeling of gene regulations
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