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September 2011 Incorporating biological information into linear models: A Bayesian approach to the selection of pathways and genes
Francesco C. Stingo, Yian A. Chen, Mahlet G. Tadesse, Marina Vannucci
Ann. Appl. Stat. 5(3): 1978-2002 (September 2011). DOI: 10.1214/11-AOAS463


The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and pathway elements involved in particular biological processes. Drug discovery efforts, for example, are focused on identifying biomarkers as well as pathways related to a disease. We propose a Bayesian model that addresses this question by incorporating information on pathways and gene networks in the analysis of DNA microarray data. Such information is used to define pathway summaries, specify prior distributions, and structure the MCMC moves to fit the model. We illustrate the method with an application to gene expression data with censored survival outcomes. In addition to identifying markers that would have been missed otherwise and improving prediction accuracy, the integration of existing biological knowledge into the analysis provides a better understanding of underlying molecular processes.


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Francesco C. Stingo. Yian A. Chen. Mahlet G. Tadesse. Marina Vannucci. "Incorporating biological information into linear models: A Bayesian approach to the selection of pathways and genes." Ann. Appl. Stat. 5 (3) 1978 - 2002, September 2011.


Published: September 2011
First available in Project Euclid: 13 October 2011

zbMATH: 1228.62150
MathSciNet: MR2884929
Digital Object Identifier: 10.1214/11-AOAS463

Keywords: Bayesian variable selection , gene expression , Markov chain Monte Carlo , Markov random field prior , pathway selection

Rights: Copyright © 2011 Institute of Mathematical Statistics


Vol.5 • No. 3 • September 2011
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