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

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2020
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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.
Reference Key
meylan2020epdnucleic Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Meylan, Patrick;Dreos, René;Ambrosini, Giovanna;Groux, Romain;Bucher, Philipp;
Journal Nucleic Acids Research
Year 2020
DOI
10.1093/nar/gkz1014
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Keywords
photoplethysmography chicken embryos heart rate measurement smartphone sensing

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