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.
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Cited in
(12)- Bayesian learning of multiple directed networks from observational data
- Bayesian genomic models for the incorporation of pathway topology knowledge into association studies
- 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
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- Modeling dependent gene expression
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