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Nucleic Acids Research Advance Access published online on May 21, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm308
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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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PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis

Li-Wei Chang1, Burr R. Fontaine2, Gary D. Stormo1,2 and Rakesh Nagarajan3,*

1Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA, 2Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA and 3Department of Pathology and Immunology, Division of Laboratory Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA

*To whom correspondence should be addressed. Tel: (314)362-8859; Fax: (314)454-5208; Email: rakesh{at}wustl.edu

Received January 31, 2007. Revised April 6, 2007. Accepted April 14, 2007.

Given the recent explosion of publications that employ microarray technology to monitor genome-wide expression and that correlate these expression changes to biological processes or to disease states, the determination of the transcriptional regulation of these co-expressed genes is the next major step toward deciphering the genetic network governing the pathway or disease under study. Although computational approaches have been proposed for this purpose, there is no integrated and user-friendly software application that allows experimental biologists to tackle this problem in higher eukaryotes. We have previously reported a systematic, statistical model of mammalian transcriptional regulatory sequence analysis. We have now made crucial extensions to this model and have developed a comprehensive, user-friendly web application suite termed the Promoter Analysis Pipeline (PAP). PAP is available at: http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do


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