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The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210552/ https://www.ncbi.nlm.nih.gov/pubmed/27899657 http://dx.doi.org/10.1093/nar/gkw1069 |
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author | Dreos, René Ambrosini, Giovanna Groux, Romain Cavin Périer, Rouaïda Bucher, Philipp |
author_facet | Dreos, René Ambrosini, Giovanna Groux, Romain Cavin Périer, Rouaïda Bucher, Philipp |
author_sort | Dreos, René |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5210552 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-52105522017-01-05 The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms Dreos, René Ambrosini, Giovanna Groux, Romain Cavin Périer, Rouaïda Bucher, Philipp Nucleic Acids Res Database Issue 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. Oxford University Press 2017-01-04 2016-11-28 /pmc/articles/PMC5210552/ /pubmed/27899657 http://dx.doi.org/10.1093/nar/gkw1069 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Dreos, René Ambrosini, Giovanna Groux, Romain Cavin Périer, Rouaïda Bucher, Philipp The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms |
title | The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms |
title_full | The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms |
title_fullStr | The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms |
title_full_unstemmed | The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms |
title_short | The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms |
title_sort | eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210552/ https://www.ncbi.nlm.nih.gov/pubmed/27899657 http://dx.doi.org/10.1093/nar/gkw1069 |
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