title: The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.
abstract: We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to the abundant release of new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) the database could be extended to plant and fungal species. We further report on the expansion of the mass genome annotation (MGA) repository containing promoter-relevant chromatin profiling data and on improvements for the EPD entry viewers. Finally, we present a new data access tool, ChIP-Extract, which enables computational biologists to extract diverse types of promoter-associated data in numerical table formats that are readily imported into statistical analysis platforms such as R.
authors.affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland rene.dreos@epfl.ch.
authors.forename: René
authors.initials: R
authors.lastname: Dreos
authors.affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.|Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Ambrosini
authors.affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Romain
authors.initials: R
authors.lastname: Groux
authors.affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Rouaïda
authors.initials: R
authors.lastname: Cavin Périer
authors.affiliation: Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.|Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D056890:Eukaryota / Q000235:genetics; D005658:Fungi / Q000235:genetics; D006801:Humans; D010944:Plants / Q000235:genetics; D011401:Promoter Regions, Genetic; D024363:Transcription Initiation Site