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Bioinformatics Vol. 19 no. 10 2003
Pages 1243-1251
© 2003 Oxford University Press

A mathematical programming approach for gene selection and tissue classification

Minghe Sun 1,* and Momiao Xiong 2

1 Department of Management Science and Statistics, College of Business, The University of Texas at San Antonio, San Antonio, TX 78249-0632, USA
2 Human Genetics Center, University of Texas-Houston Health Science Center, Houston, Boston, TX 77225, USA

Received on July 29, 2002 ; revised on November 13, 2002 and January 8, 2003 ; accepted on January 21, 2003

Motivation: Extracting useful information from expression levels of thousands of genes generated with microarry technology needs a variety of analytical techniques. Mathematical programming approaches for classification analysis outperform parametric methods when the data depart from assumptions underlying these methods. Therefore, a mathematical programming approach is developed for gene selection and tissue classification using gene expression profiles.

Results: A new mixed integer programming model is formulated for this purpose. The mixed integer programming model simultaneously selects genes and constructs a classification model to classify two groups of tissue samples as accurately as possible. Very encouraging results were obtained with two data sets from the literature as examples. These results show that the mathematical programming approach can rival or outperform traditional classification methods.

Contact: msun{at}utsa.edu

* To whom correspondence should be addressed.


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