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Title: ORegAnno: an open-access community-driven resource for regulatory annotation
Authors: Griffith, Obi L
Montgomery, Stephen B
Bernier, Bridget
Chu, Bryan
Kasaian, Katayoon
Aerts, Stein
Mahony, Shaun
Sleumer, Monica C
Bilenky, Mikhail
Haeussler, Maximilian
Griffith, Malachi
Gallo, Steven M
Giardine, Belinda
Hooghe, Bart
Van Loo, Peter
Blanco, Enrique
Ticoll, Amy
Lithwick, Stuart
Portales-Casamar, Elodie
Donaldson, Ian J
Robertson, Gordon
Wadelius, Claes
De Bleser, Pieter
Vlieghe, Dominique
Halfon, Marc S
Wasserman, Wyeth
Hardison, Ross
Bergman, Casey M
Jones, Steven J. M # ×
Issue Date: Jan-2008
Publisher: Oxford univ press
Series Title: Nucleic acids research vol:36 pages:D107-D113
Abstract: ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the publication queue allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or check out papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org.
ISSN: 0305-1048
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Neurogenetics
Human Genome Laboratory
Department of Human Genetics - miscellaneous
× corresponding author
# (joint) last author

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