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Nucleic Acids Res. 2017 Jan 4;45(D1):D51-D55. doi: 10.1093/nar/gkw1069. Epub 2016 Nov 28.

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.

Author information

1
Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland rene.dreos@epfl.ch.
2
Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
3
Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.

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.

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