RAEdb: a database of enhancers identified by high-throughput reporter assays

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.

[1]  A. Visel,et al.  Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development , 2013, Cell.

[2]  Dennis B. Troup,et al.  NCBI GEO: archive for functional genomics data sets—10 years on , 2010, Nucleic Acids Res..

[3]  Xia Li,et al.  DiseaseEnhancer: a resource of human disease-associated enhancer catalog , 2017, Nucleic Acids Res..

[4]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[5]  T. Mikkelsen,et al.  Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. , 2013, Genome research.

[6]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[7]  Łukasz M. Boryń,et al.  STARR-seq - principles and applications. , 2015, Genomics.

[8]  M. Levine.  Transcriptional Enhancers in Animal Development and Evolution , 2010, Current Biology.

[9]  Łukasz M. Boryń,et al.  Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.

[10]  Derek W Wright,et al.  Gateways to the FANTOM5 promoter level mammalian expression atlas , 2015, Genome Biology.

[11]  D. Matallanas,et al.  Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis. , 2016, Cell stem cell.

[12]  T. Mikkelsen,et al.  Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay , 2012, Nature Biotechnology.

[13]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[14]  D. Gifford,et al.  Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET , 2008, Genome Biology.

[15]  N. Ahituv,et al.  Decoding enhancers using massively parallel reporter assays. , 2015, Genomics.

[16]  Vladimir B. Bajic,et al.  DENdb: database of integrated human enhancers , 2015, Database J. Biol. Databases Curation.

[17]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[18]  Lan T M Dao,et al.  Genome-wide characterization of mammalian promoters with distal enhancer functions , 2017, Nature Genetics.

[19]  Bin Zhang,et al.  SEA: a super-enhancer archive , 2015, Nucleic Acids Res..

[20]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[21]  B. Tjaden,et al.  De novo assembly of bacterial transcriptomes from RNA-seq data , 2015, Genome Biology.

[22]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[23]  Aziz Khan,et al.  dbSUPER: a database of super-enhancers in mouse and human genome , 2015, bioRxiv.

[24]  Hideaki Sugawara,et al.  Archiving next generation sequencing data , 2009, Nucleic Acids Res..

[25]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

[26]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[27]  Bing He,et al.  EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types , 2016, Bioinform..