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Nucleic Acids Research Advance Access published online on June 21, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm327
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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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Onto-Tools: new additions and improvements in 2006

Purvesh Khatri1, Calin Voichita1, Khalid Kattan1, Nadeem Ansari1, Avani Khatri1, Constantin Georgescu1, Adi L. Tarca2 and Sorin Draghici1,*

1Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and 2Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA

*To whom correspondence should be addressed. Tel: +1 313 577 5484; Fax: +1 313 577 6868; Email: sorin{at}wayne.edu

Received January 31, 2007. Revised April 10, 2007. Accepted April 17, 2007.

Onto-Tools is a freely available web-accessible software suite, composed of an annotation database and nine complementary data-mining tools. This article describes a new tool, Onto-Express-to-go (OE2GO), as well as some new features implemented in Pathway-Express and Onto-Miner over the past year. Pathway-Express (PE) has been enhanced to identify significantly perturbed pathways in a given condition using the differentially expressed genes in the input. OE2GO is a tool for functional profiling using custom annotations. The development of this tool was aimed at the researchers working with organisms for which annotations are not yet available in the public domain. OE2GO allows researchers to use either annotation data from the Onto-Tools database, or their own custom annotations. By removing the necessity to use any specific database, OE2GO makes the functional profiling available for all organisms, with annotations using any ontology. The Onto-Tools are freely available at http://vortex.cs.wayne.edu/projects.htm.


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