The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.
Bottom Line: EPDnew is a collection of automatically compiled, organism-specific promoter lists complementing the old corpus of manually compiled promoter entries of EPD.This new part is exclusively derived from next generation sequencing data from high-throughput promoter mapping experiments.We report on the recent growth of EPDnew, its extension to additional model organisms and its improved integration with other bioinformatics resources developed by our group, in particular the Signal Search Analysis and ChIP-Seq web servers.
Affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.Show MeSH
Related in: MedlinePlus
Mentions: The web services directly linked to EPD perform two types of tasks: promoter analysis and subset selection. ChIP-Cor from the ChIP-Seq server is an analysis tool which generates aggregation plots (18) for two genomic features, called reference and target feature. (The generic term feature covers everything that can be mapped to a genome position, e.g. TSSs, mapped ChIP-Seq reads, etc.). The server returns a graph showing the positional distribution of the target features relative to the reference feature (see example in Figure 1b based on data from 19). The web-interface allows users to choose any sample from the MGA repository as a target or reference feature. Alternatively, features can be uploaded as a genome annotation format file in BED, GFF or BAM format. If ChIP-Cor is accessed directly from an organism-specific EPDnew home page, the corresponding promoter collection will automatically appear as the default reference feature in the ChIP-Cor input format.
Affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.