Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes
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Publication:652363
DOI10.1214/11-AOAS463zbMATH Open1228.62150arXiv1111.5419OpenAlexW3101256146WikidataQ40614440 ScholiaQ40614440MaRDI QIDQ652363FDOQ652363
Authors: Francesco C. Stingo, Yian A. Chen, Mahlet G. Tadesse, Marina Vannucci 
Publication date: 14 December 2011
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
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.
Full work available at URL: https://arxiv.org/abs/1111.5419
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Bayesian inference (62F15) Censored data models (62N01) Applications of statistics to biology and medical sciences; meta analysis (62P10) Numerical analysis or methods applied to Markov chains (65C40) Biochemistry, molecular biology (92C40)
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