Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data

DOI10.1214/10-AOAS425zbMATH Open1223.62014arXiv1108.0793OpenAlexW3099110849WikidataQ34097779 ScholiaQ34097779MaRDI QIDQ641127FDOQ641127

Hongyu Zhao, Ruiyan Luo

Publication date: 21 October 2011

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

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.

Full work available at URL: https://arxiv.org/abs/1108.0793

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zbMATH Keywords

Markov chain Monte CarloGaussian graphical modelBayesian networkhierarchical modelmixture distributiondependency networksignaling pathwaysingle cell measurements

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Numerical analysis or methods applied to Markov chains (65C40) Biochemistry, molecular biology (92C40) Cell biology (92C37)

Cites Work

• Sparse graphical models for exploring gene expression data
• Being Bayesian about network structure. A Bayesian approach to structure discovery in Bayesian networks
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• Learning Causal Bayesian Network Structures From Experimental Data
• Dependency networks for inference, collaborative filtering, and data visualization
• A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
• Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data

Cited In (5)

• Objective Bayes model selection of Gaussian interventional essential graphs for the identification of signaling pathways
• 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
• Title not available (Why is that?)

Uses Software

• HdBCS

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