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Bioinformatics Vol. 19 no. 1 2003
Pages 71-78
© 2003 Oxford University Press

Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients

Jinyan Li 1,*, Huiqing Liu 1, James R. Downing 2, Allen Eng-Juh Yeoh 3 and Limsoon Wong 1

1 Laboratories for Information Technology, 21 Heng Mui Keng Terrace, Singapore 119613
2 St Jude Children’s Research Hospital, Memphis, TN 38105, USA
3 National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074

Received on March 19, 2002 ; revised on June 19, 2002 and July 18, 2002 ; accepted on July 21, 2002

Motivations and Results: For classifying gene expression profiles or other types of medical data, simple rules are preferable to non-linear distance or kernel functions. This is because rules may help us understand more about the application in addition to performing an accurate classification. In this paper, we discover novel rules that describe the gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. We also introduce a new classifier, named PCL, to make effective use of the rules. PCL is accurate and can handle multiple parallel classifications. We evaluate this method by classifying 327 heterogeneous ALL samples. Our test error rate is competitive to that of support vector machines, and it is 71% better than C4.5, 50% better than Naive Bayes, and 43% better than k-nearest neighbour. Experimental results on another independent data sets are also presented to show the strength of our method.

Availability: Under http://sdmc.lit.org.sg/GEDatasets/, click on Supplementary Information.

Contact: jinyan{at}lit.a-star.edu.sg

* To whom correspondence should be addressed.


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