The Annals of Applied Statistics

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, and Marina Vannucci

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Abstract

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.

Article information

Source
Ann. Appl. Stat., Volume 5, Number 3 (2011), 1978-2002.

Dates
First available in Project Euclid: 13 October 2011

Permanent link to this document
https://projecteuclid.org/euclid.aoas/1318514292

Digital Object Identifier
doi:10.1214/11-AOAS463

Mathematical Reviews number (MathSciNet)
MR2884929

Zentralblatt MATH identifier
1228.62150

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

Citation

Stingo, Francesco C.; Chen, Yian A.; Tadesse, Mahlet G.; Vannucci, Marina. Incorporating biological information into linear models: A Bayesian approach to the selection of pathways and genes. Ann. Appl. Stat. 5 (2011), no. 3, 1978--2002. doi:10.1214/11-AOAS463. https://projecteuclid.org/euclid.aoas/1318514292


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