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Nucleic Acids Research Advance Access published online on June 18, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm427
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© 2007 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.

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oPOSSUM: integrated tools for analysis of regulatory motif over-representation

Shannan J. Ho Sui1,2, Debra L. Fulton1,2, David J. Arenillas1,3, Andrew T. Kwon1,2 and Wyeth W. Wasserman1,3,*

1Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, 2Genetics Graduate Program and 3Department of Medical Genetics, University of British Columbia, Vancouver BC, Canada

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

Received January 31, 2007. Revised April 13, 2007. Accepted May 10, 2007.

The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an internet-based system for such studies of regulation, has been improved and expanded in this new release. New features include a worm-specific version for investigating binding sites conserved between Caenorhabditis elegans and C. briggsae, as well as a yeast-specific version for the analysis of co-expressed sets of Saccharomyces cerevisiae genes. The human and mouse applications feature improvements in ortholog mapping, sequence alignments and the delineation of multiple alternative promoters. oPOSSUM2, introduced for the analysis of over-represented combinations of motifs in human and mouse genes, has been integrated with the original oPOSSUM system. Analysis using user-defined background gene sets is now supported. The transcription factor binding site models have been updated to include new profiles from the JASPAR database. oPOSSUM is available at http://www.cisreg.ca/oPOSSUM/


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