AI Article Synopsis
- The Eukaryotic Promoter Database (EPD) update focuses on the EPDnew section, featuring extensive collections of transcription start sites (TSS) derived from next-generation sequencing data.
- The database now includes promoter data for plant and fungal species due to the influx of high-throughput transcript mapping technologies like CAGE and TSS-seq.
- A new tool called ChIP-Extract was introduced, allowing biologists to easily access and extract promoter-related data for use in statistical analysis tools like R.
Article 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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|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210552 | PMC |
| http://dx.doi.org/10.1093/nar/gkw1069 | DOI Listing |
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