ArticleNucleic acids research2013
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
95 citing papers in PubMed, 2 syntheses or guidelines pooled it, 173 citations in OpenAlex.
- Genetic determinants of skin ageing: a systematic review and meta-analysis of genome-wide association studies and candidate genes.Journal of physiological anthropology · 2025Pooled it
- Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment.BMC cancer · 2016Pooled it
- Serpin peptidase inhibitor (SERPINB5) haplotypes are associated with susceptibility to hepatocellular carcinoma.Scientific reports · 2016Trial
- Pan-cancer multi-omics analysis reveals upregulation of the POLE2 subunit of DNA polymerase epsilon and its associations with patient survival and cellular pathways beyond DNA replication.NAR genomics and bioinformatics · 2026Article
- Single-allele nanoscale mapping of regulatory variants.Nature genetics · 2026Article
- Dynamic NFIX Promoter Usage Shapes Stem and Committed Myogenic States.International journal of molecular sciences · 2026Article
- DNA Sequence Perplexity Reveals Evolutionarily Conserved Patterns in cis-Regulatory Regions Across Diverse Species.Biochemical genetics · 2026Article
- Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes.bioRxiv : the preprint server for biology · 2026Article
- A microRNA expression signature in infant t(4;11) KMT2A::AFF1+ BCP-ALL uncovers novel therapeutic targets.HemaSphere · 2026Article
- Large language models for bioinformatics.Quantitative biology (Beijing, China) · 2026Review
- Optimizing genomic language models for promoter prediction: a comparative study of tokenization and cross-species learning.NAR genomics and bioinformatics · 2026Article
- Foxn3 is part of a transcriptional network that regulates primary cilia in the developing retina.Development (Cambridge, England) · 2026Article
- Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms inInternational journal of molecular sciences · 2025Article
- TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction.Bioinformatics (Oxford, England) · 2025Article
- A microRNA CRISPR screen reveals microRNA-483-3p as an apoptotic regulator in prostate cancer cells.Cell death & disease · 2025Article
- A distal promoter and aberrant splicing enable canonical translation of out-of-frame proteins in Huntington's disease.bioRxiv : the preprint server for biology · 2025Article
- The significance of PAX5 in Merkel cell carcinoma.The Journal of pathology · 2025Article
- Review
- DNA promoter task-oriented dictionary mining and prediction model based on natural language technology.Scientific reports · 2025Article
- Characterization and visualization of tandem repeats at genome scale.Nature biotechnology · 2024Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in the genome, typically the major transcription start site (TSS). EPD primarily serves biologists interested in analysing the motif content, chromatin structure or DNA methylation status of co-regulated promoter subsets. Initially, promoter evidence came from TSS mapping experiments targeted at single genes and published in journal articles. Today, the TSS positions provided by EPD are inferred from next-generation sequencing data distributed in electronic form. Traditionally, EPD has been a high-quality database with low coverage. The focus of recent efforts has been to reach complete gene coverage for important model organisms. To this end, we introduced a new section called EPDnew, which is automatically assembled from multiple, carefully selected input datasets. As another novelty, we started to use chromatin signatures in addition to mRNA 5'tags to locate promoters of weekly expressed genes. Regarding user interfaces, we introduced a new promoter viewer which enables users to explore promoter-defining experimental evidence in a UCSC genome browser window.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.