Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data
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Abstract: Recent technological advances have made it possible to simultaneously measure multiple protein activities at the single cell level. With such data collected under different stimulatory or inhibitory conditions, it is possible to infer the causal relationships among proteins from single cell interventional data. In this article we propose a Bayesian hierarchical modeling framework to infer the signaling pathway based on the posterior distributions of parameters in the model. Under this framework, we consider network sparsity and model the existence of an association between two proteins both at the overall level across all experiments and at each individual experimental level. This allows us to infer the pairs of proteins that are associated with each other and their causal relationships. We also explicitly consider both intrinsic noise and measurement error. Markov chain Monte Carlo is implemented for statistical inference. We demonstrate that this hierarchical modeling can effectively pool information from different interventional experiments through simulation studies and real data analysis.
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Cites work
- scientific article; zbMATH DE number 1134987 (Why is no real title available?)
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- Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data
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Cited in
(8)- Causal inference in biomolecular pathways using a Bayesian network approach and an implicit method
- A linear programming model based on network flow for pathway inference
- Objective Bayes model selection of Gaussian interventional essential graphs for the identification of signaling pathways
- Learning causal networks via additive faithfulness
- Refining cellular pathway models using an ensemble of heterogeneous data sources
- Likelihood ratio tests for a large directed acyclic graph
- Corrected score methods for estimating Bayesian networks with error-prone nodes
- Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data
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