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Bioinformatics Advance Access published online on January 5, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk027
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 25, 2005
Revised December 22, 2005
Accepted December 23, 2005

Applications note

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation

Montgomery S. B. 1, Griffith O. L. 1, Sleumer M. C. 1, Bergman C. M. 2, Bilenky M. 1, Pleasance E. D. 1, Prychyna Y. 1, Zhang X. 1, and Jones S. J. M. 1 *

1 Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100-570 West 7th Avenue, Vancouver, BC, Canada, V5Z 4E6
2 Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, M13 9PT, Manchester, UK

* To whom correspondence should be addressed.
Jones S. J. M., E-mail: sjones{at}bcgsc.ca


  Abstract

Motivation: Our understanding of gene regulation is currently limited by our ability to collectively synthesize and catalogue transcriptional regulatory elements stored in scientific literature. Over the past decade, this task has become increasingly challenging as the accrual of biologically-validated regulatory sequences has accelerated. To meet this challenge, novel community-based approaches to regulatory element annotation are required.

Summary: Here, we present the Open Regulatory Annotation (ORegAnno) database as a dynamic collection of literature-curated regulatory regions, transcription factor binding sites and regulatory mutations (polymorphisms and haplotypes). ORegAnno has been designed to manage the submission, indexing and validation of new annotations from users worldwide. Submissions to ORegAnno are immediately cross-referenced to EnsEMBL, dbSNP, Entrez Gene, the NCBI Taxonomy database and PubMed, where appropriate.

Availability: ORegAnno is available directly through MySQL, Web services, and online at http://www.oreganno.org. All software is licensed under the Lesser GNU Public License (LGPL).

1These authors contributed equally to this work

Associate Editor: Nikolaus Rajewsky


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