Modeling dependent gene expression

DOI10.1214/11-AOAS525zbMATH Open1243.62038arXiv1206.6650WikidataQ38803187 ScholiaQ38803187MaRDI QIDQ439142FDOQ439142

Giovanni Parmigiani, Donatello Telesca, P. Müller, Ralph S. Freedman

Publication date: 1 August 2012

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: In this paper we propose a Bayesian approach for inference about dependence of high throughput gene expression. Our goals are to use prior knowledge about pathways to anchor inference about dependence among genes; to account for this dependence while making inferences about differences in mean expression across phenotypes; and to explore differences in the dependence itself across phenotypes. Useful features of the proposed approach are a model-based parsimonious representation of expression as an ordinal outcome, a novel and flexible representation of prior information on the nature of dependencies, and the use of a coherent probability model over both the structure and strength of the dependencies of interest. We evaluate our approach through simulations and in the analysis of data on expression of genes in the Complement and Coagulation Cascade pathway in ovarian cancer.

Full work available at URL: https://arxiv.org/abs/1206.6650

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zbMATH Keywords

probit modelsconditional independencemicroarray dataprobability of expressionreciprocal graphsreversible jumps MCMC

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)

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Cited In (8)

• Bayesian learning of multiple directed networks from observational data
• Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes
• Inferring gene dependency networks from genomic longitudinal data: a functional data approach
• Reciprocal graphical models for integrative gene regulatory network analysis
• Bayesian selection of graphical regulatory models
• Modeling dependent gene expression
• An Integrative Bayesian Modeling Approach to Imaging Genetics
• Bayesian Analysis of Curves Shape Variation Through Registration and Regression

Uses Software

• GOSim
• HdBCS

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