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EPDnew specifications


Unique identifier OMICS_06211
Name EPDnew
Restrictions to use None
Maintained Yes


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
  • Vertebrates
    • Danio rerio


  • person_outline Philipp Bucher

Publications for EPDnew

EPDnew citations


Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

PLoS Genet
PMCID: 5628936
PMID: 28945760
DOI: 10.1371/journal.pgen.1007001

[…] tium Human Build 37.p13 (GRCh37.p13).The mutational screen of homozygous loss was performed in any region that had a homozygous loss in at least one sample. For mutations that occur within promoters, EPDNew human version 003 [] was used to define promoter regions. Conserved regions of DNA were determined from UCSC phastCons scores for multiple alignments of 45 vertebrate genomes to the hg19 human […]


Oxidative stress rapidly stabilizes promoter proximal paused Pol II across the human genome

Nucleic Acids Res
PMCID: 5737879
PMID: 28977633
DOI: 10.1093/nar/gkx724

[…] The hg19 EPDnew promoter database () was filtered to eliminate duplicate TSS and entries with a neighboring TSS within 1 kb (leaving 17592 TSS). For PRO-Seq, fragment lengths were recorded if their 5′ ends wer […]


OSBPL10, RXRA and lipid metabolism confer African ancestry protection against dengue haemorrhagic fever in admixed Cubans

PLoS Pathog
PMCID: 5344536
PMID: 28241052
DOI: 10.1371/journal.ppat.1006220

[…] ther measure of positive selection (XP-EHH—detects selective sweeps above 80% frequency) was applied to the Cuban HCG.The significant SNPs were ascertained for location in regulatory regions by using EPDNew [] and HaploReg [] tools. EDPNew comprises organism-specific (we obviously used H. sapiens) transcription start site (TSS) collections automatically assembled from carefully selected mass seque […]


Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks

PLoS One
PMCID: 5291440
PMID: 28158264
DOI: 10.1371/journal.pone.0171410

[…] re the sensitivity of 58% and specificity of 92% with correlation coefficient (CC) in the range of 0.52–0.73 were observed [].In this work, we studied sequences of promoter regions extracted from the EPDnew promoter database [], which recently extended promoter collection beyond cases based on evidence from TSS mapping experiments on single genes. Currently, TSS positions provided by EPD are infer […]


The KDM5 family is required for activation of pro proliferative cell cycle genes during adipocyte differentiation

Nucleic Acids Res
PMCID: 5389521
PMID: 27899593
DOI: 10.1093/nar/gkw1156

[…] Cruz (UCSC) Genome Browser () was used for visualization of genome tracks. For analyses of promoter features, we retrieved 2,742 promoters containing TATA boxes from the Eukaryotic Promoter Database (EPDnew) (). We overlapped these promoter sequences with the respective gene groups and considered a gene as having a TATA box in the promoter if it was found within ±100 bp of the TSS of the RefSeq-an […]


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

Nucleic Acids Res
PMCID: 5210552
PMID: 27899657
DOI: 10.1093/nar/gkw1069

[…] The content of EPDnew has substantially increased over the last two years. In our previous paper (), we presented promoter collections for five model organisms, all animals (Homo sapiens, Mus musculus, Drosophila me […]


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EPDnew institution(s)
Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland

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