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. 2004 Jan 1;32(Database issue):D82-5.
doi: 10.1093/nar/gkh122.

The Eukaryotic Promoter Database EPD: The Impact of in Silico Primer Extension

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Free PMC article

The Eukaryotic Promoter Database EPD: The Impact of in Silico Primer Extension

Christoph D Schmid et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1
Figure 1
In silico primer extension yields results comparable to those of conventional methods. The upper panel displays the frequency distribution of the 5′ends of transcripts of the human aldolase A gene as derived from DBTSS (9). The figure in the lower panel [reprinted from (11) with permission from Elsevier] summarizes the results of mRNA 5′end mapping experiments carried out by conventional techniques for the same gene. Note that in silico primer extension successfully identified all four promoter regions reported before.
Figure 2
Figure 2
TATA and CCAAT box occurrence profiles for three classes of promoter entry. The DBTSS and MGC subsets were derived by in silico primer extension. The definitions of the sequence motifs were taken from (2). The TATA and CCAAT box signals were searched for in sliding windows of 20 and 50 bp, respectively. Theses profiles have been produced with the Signal search analysis server (14).

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