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Nucleic Acids Research Advance Access originally published online on October 29, 2008
Nucleic Acids Research 2009 37(Database issue):D54-D60; doi:10.1093/nar/gkn783
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Nucleic Acids Research, 2009, Vol. 37, Database issue D54-D60
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

Elodie Portales-Casamar1, David Arenillas1, Jonathan Lim1, Magdalena I. Swanson1, Steven Jiang1, Anthony McCallum1, Stefan Kirov2 and Wyeth W. Wasserman1,*

1Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada and 2Applied Genomics Department, Pharmaceutical Research Institute, Bristol-Myers Squibb, NJ, USA

*To whom correspondence should be addressed. Tel: +1 (604) 875 3812; Fax: +1 (604) 875 3819; Email: wyeth{at}cmmt.ubc.ca

Received September 9, 2008. Revised October 9, 2008. Accepted October 9, 2008.

The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein–DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ‘boutiques’ within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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E. Portales-Casamar, S. Thongjuea, A. T. Kwon, D. Arenillas, X. Zhao, E. Valen, D. Yusuf, B. Lenhard, W. W. Wasserman, and A. Sandelin
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
Nucleic Acids Res., January 1, 2010; 38(suppl_1): D105 - D110.
[Abstract] [Full Text] [PDF]


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