000183818 001__ 183818
000183818 005__ 20190316235551.0
000183818 0247_ $$2doi$$a10.1093/nar/gks1233
000183818 022__ $$a0305-1048
000183818 02470 $$2ISI$$a000312893300022
000183818 037__ $$aARTICLE
000183818 245__ $$aEPD and EPDnew, high-quality promoter resources in the next-generation sequencing era
000183818 269__ $$a2013
000183818 260__ $$bOxford University Press$$c2013$$aOxford
000183818 300__ $$a8
000183818 336__ $$aJournal Articles
000183818 520__ $$aThe Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in the genome, typically the major transcription start site (TSS). EPD primarily serves biologists interested in analysing the motif content, chromatin structure or DNA methylation status of co-regulated promoter subsets. Initially, promoter evidence came from TSS mapping experiments targeted at single genes and published in journal articles. Today, the TSS positions provided by EPD are inferred from next-generation sequencing data distributed in electronic form. Traditionally, EPD has been a high-quality database with low coverage. The focus of recent efforts has been to reach complete gene coverage for important model organisms. To this end, we introduced a new section called EPDnew, which is automatically assembled from multiple, carefully selected input datasets. As another novelty, we started to use chromatin signatures in addition to mRNA 5'tags to locate promoters of weekly expressed genes. Regarding user interfaces, we introduced a new promoter viewer which enables users to explore promoter-defining experimental evidence in a UCSC genome browser window.
000183818 700__ $$0(EPFLAUTH)211511$$g211511$$aDreos, René
000183818 700__ $$0243605$$g176602$$aAmbrosini, Giovanna
000183818 700__ $$0(EPFLAUTH)112989$$g112989$$aCavin Perier, Rouayda
000183818 700__ $$0244404$$g113607$$aBucher, Philipp
000183818 773__ $$j41$$tNucleic Acids Research$$kD1$$qD157-64
000183818 8564_ $$uhttps://infoscience.epfl.ch/record/183818/files/Nucl.%20Acids%20Res.-2013-Dreos-D157-64.pdf$$zPublisher's version$$s4087442$$yPublisher's version
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000183818 937__ $$aEPFL-ARTICLE-183818
000183818 973__ $$rREVIEWED$$sPUBLISHED$$aEPFL
000183818 980__ $$aARTICLE