ArticleNucleic acids research2004
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 95 citations in OpenAlex.
- Article
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- The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.Nucleic acids research · 2017Article
- The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.Nucleic acids research · 2015Article
- EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.Nucleic acids research · 2013Article
- Towards biological characters of interactions between transcription factors and their DNA targets in mammals.BMC genomics · 2012Article
- Discovery of functional gene variants associated with human longevity: opportunities and challenges.The journals of gerontology. Series A, Biological sciences and medical sciences · 2012Article
- Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis.BMC genomics · 2011Article
- The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.Database : the journal of biological databases and curation · 2010Article
- Phylogeny disambiguates the evolution of heat-shock cis-regulatory elements in Drosophila.PloS one · 2010Article
- Contrasting patterns of transposable element insertions in Drosophila heat-shock promoters.PloS one · 2009Article
- Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups.BMC genomics · 2009Article
- Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.Genome biology · 2009Article
- MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.Nucleic acids research · 2007Article
- PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.Genome biology · 2007Article
- Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism.Nucleic acids research · 2007Article
- A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1.Genome research · 2006Article
- The features of Drosophila core promoters revealed by statistical analysis.BMC genomics · 2006Article
- AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.BMC bioinformatics · 2006Article
- TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences.Nucleic acids research · 2006Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.
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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.