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Bioinformatics Advance Access originally published online on January 5, 2006
Bioinformatics 2006 22(5):637-640; 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
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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

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

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

*To whom correspondence should be addressed.

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).

Contact: sjones{at}bcgsc.ca

Received on October 25, 2005; revised on December 22, 2005; accepted on December 23, 2005

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