The Eukaryotic Promoter Database (EPD)

R. C. Perier

doi:10.1093/nar/28.1.302

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension

Nucleic Acids Research ◽

10.1093/nar/gkh122 ◽

2004 ◽

Vol 32 (90001) ◽

pp. 82D-85 ◽

Cited By ~ 48

Author(s):

C. D. Schmid

Keyword(s):

In Silico ◽

Primer Extension ◽

Eukaryotic Promoter ◽

Eukaryotic Promoter Database ◽

The Impact

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The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Nucleic Acids Research ◽

10.1093/nar/gkw1069 ◽

2016 ◽

Vol 45 (D1) ◽

pp. D51-D55 ◽

Cited By ~ 66

Author(s):

René Dreos ◽

Giovanna Ambrosini ◽

Romain Groux ◽

Rouaïda Cavin Périer ◽

Philipp Bucher

Keyword(s):

Eukaryotic Promoter ◽

Eukaryotic Promoter Database

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EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Nucleic Acids Research ◽

10.1093/nar/gkz1014 ◽

2019 ◽

Cited By ~ 1

Author(s):

Patrick Meylan ◽

René Dreos ◽

Giovanna Ambrosini ◽

Romain Groux ◽

Philipp Bucher

Keyword(s):

Ucsc Genome Browser ◽

Genome Browser ◽

Model Organisms ◽

Similar Data ◽

Web Interfaces ◽

Eukaryotic Promoter ◽

Human Promoter ◽

Eukaryotic Promoter Database ◽

A Genome ◽

Human And Mouse

Abstract The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats (FASTA, BED, CSV) for subsequent analysis with other tools. Recent work has focused on the improvement of the EPD promoter viewers, which use the UCSC Genome Browser as visualization platform. Thousands of high-resolution tracks for CAGE, ChIP-seq and similar data have been generated and organized into public track hubs. Customized, reproducible promoter views, combining EPD-supplied tracks with native UCSC Genome Browser tracks, can be accessed from the organism summary pages or from individual promoter entries. Moreover, thanks to recent improvements and stabilization of ncRNA gene catalogs, we were able to release promoter collections for certain classes of ncRNAs from human and mouse. Furthermore, we developed automatic computational protocols to assign orphan TSS peaks to downstream genes based on paired-end (RAMPAGE) TSS mapping data, which enabled us to add nearly 9000 new entries to the human promoter collection. Since our last article in this journal, EPD was extended to five more model organisms: rhesus monkey, rat, dog, chicken and Plasmodium falciparum.

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The UCSC Genome Browser database: 2021 update

Nucleic Acids Research ◽

10.1093/nar/gkaa1070 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D1046-D1057 ◽

Cited By ~ 1

Author(s):

Jairo Navarro Gonzalez ◽

Ann S Zweig ◽

Matthew L Speir ◽

Daniel Schmelter ◽

Kate R Rosenbloom ◽

...

Keyword(s):

New Technologies ◽

Ucsc Genome Browser ◽

Regulatory Elements ◽

Genome Browser ◽

Eukaryotic Promoter ◽

Ucsc Genome Browser Database ◽

Eukaryotic Promoter Database ◽

A Genome ◽

Ncbi Refseq ◽

Genome Annotations

Abstract For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

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