Bioinformatics Vol. 19 no. 1 2003
Pages 90-97
© 2003 Oxford University Press
Gene selection: a Bayesian variable selection approach
1 Department of Statistics, Texas A&M University,
College Station, TX 77843-3143, USA
2 Department of Electrical Engineering, Texas A&M University,
College Station, TX 77840, USA
3 Department of Pathology, University of Texas,
M. D. Anderson Cancer Center, USA
4 Mathematical Sciences Department, University of Texas at El Paso,
USA
Received on January 24, 2002
; revised on April 29, 2002
; accepted on June 17, 2002
Selection of significant genes via expression patterns is an important problem in microarray experiments. Owing to small sample size and the large number of variables (genes), the selection process can be unstable. This paper proposes a hierarchical Bayesian model for gene (variable) selection. We employ latent variables to specialize the model to a regression setting and uses a Bayesian mixture prior to perform the variable selection. We control the size of the model by assigning a prior distribution over the dimension (number of significant genes) of the model. The posterior distributions of the parameters are not in explicit form and we need to use a combination of truncated sampling and Markov Chain Monte Carlo (MCMC) based computation techniques to simulate the parameters from the posteriors. The Bayesian model is flexible enough to identify significant genes as well as to perform future predictions. The method is applied to cancer classification via cDNA microarrays where the genes BRCA1 and BRCA2 are associated with a hereditary disposition to breast cancer, and the method is used to identify a set of significant genes. The method is also applied successfully to the leukemia data.
Supplementary information: http://stat.tamu.edu/people/faculty/bmallick.html
Contact: bmallick{at}stat.tanu.edu
* To whom correspondence should be addressed.
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