Bioinformatics Vol. 18 no. 4 2002
Pages 566-575
© 2002 Oxford University Press
Application of Bayesian Decomposition for analysing microarray data
1 Bioinformatics Working Group, Fox Chase
Cancer Center, Philadelphia, PA 19111, USA
2 Department of Biology, Beckman Research
Institute of the City of Hope, Duarte, CA 91010, USA
3 Bioinformatics Facility, Fox Chase Cancer
Center, Philadelphia, PA 19111, USA
Received on October 1, 2001
; revised on October 31, 2001
; accepted on November 7, 2001
Motivation: Microarray and gene chip technology provide high throughput tools for measuring gene expression levels in a variety of circumstances, including cellular response to drug treatment, cellular growth and development, tumorigenesis, among many other processes. In order to interpret the large data sets generated in experiments, data analysis techniques that consider biological knowledge during analysis will be extremely useful. We present here results showing the application of such a tool to expression data from yeast cell cycle experiments.
Results: Originally developed for spectroscopic analysis,
Bayesian Decomposition (BD) includes two features which make it
useful for microarray data analysis: the ability to assign genes to
multiple coexpression groups and the ability to encode biological
knowledge into the system. Here we demonstrate the ability of the
algorithm to provide insight into the yeast cell cycle, including
identification of five temporal patterns tied to cell cycle phases
as well as the identification of a pattern tied to an 
40 min cell cycle oscillator. The genes are simultaneously
assigned to the patterns, including partial assignment to multiple
patterns when this is required to explain the expression
profile.
Availability: The application is available free to academic users under a material transfer agreement. Go to http://bioinformatics.fccc.edu/ for more details.
Contact: td_ moloshok{at}fccc.edu; RKlevecz{at}coh.org; jd_ grant{at}fccc.edu; fj_ manion{at}fccc.edu; speier1{at}prodigy.net; m_ ochs{at}fccc.edu
* To whom correspondence should be addressed.
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