A Bayesian graphical modeling approach to microRNA regulatory network inference

DOI10.1214/10-AOAS360zbMATH Open1220.62142arXiv1101.1377WikidataQ37089017 ScholiaQ37089017MaRDI QIDQ542971FDOQ542971

Authors: Francesco C. Stingo, Yian A. Chen, Marianne Barrier, Philip E. Mirkes, Marina Vannucci 

Publication date: 20 June 2011

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

Abstract: It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs are called targets. Typically, methods for target prediction are based solely on sequence data and on the structure information. In this paper we propose a Bayesian graphical modeling approach that infers the miRNA regulatory network by integrating expression levels of miRNAs with their potential mRNA targets and, via the prior probability model, with their sequence/structure information. We use a directed graphical model with a particular structure adapted to our data based on biological considerations. We then achieve network inference using stochastic search methods for variable selection that allow us to explore the huge model space via MCMC. A time-dependent coefficients model is also implemented. We consider experimental data from a study on a very well-known developmental toxicant causing neural tube defects, hyperthermia. Some of the pairs of target gene and miRNA we identify seem very plausible and warrant future investigation. Our proposed method is general and can be easily applied to other types of network inference by integrating multiple data sources.

Full work available at URL: https://arxiv.org/abs/1101.1377

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zbMATH Keywords

data integrationgraphical modelsBayesian variable selectionmiRNA regulatory network

Mathematics Subject Classification ID

Bayesian inference (62F15) Multivariate analysis (62H99) Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of graph theory (05C90) Biochemistry, molecular biology (92C40) Search theory (90B40)

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Cited In (30)

• Bayesian learning of multiple directed networks from observational data
• Title not available (Why is that?)
• miRNA-target gene regulatory networks: a Bayesian integrative approach to biomarker selection with application to kidney cancer
• A novel Bayesian multiple testing approach to deregulated miRNA discovery harnessing positional clustering
• Hierarchical normalized completely random measures for robust graphical modeling
• Bayesian Lesion Estimation with a Structured Spike-and-Slab Prior
• Sparse inverse covariance estimation for high-throughput microRNA sequencing data in the Poisson log-normal graphical model
• MicroRNA Regulatory Network: Structure and Function
• Bayesian approaches for large biological networks
• A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes
• Bayesian graphical models for modern biological applications
• Response variable selection in multivariate linear regression
• Latent Network Estimation and Variable Selection for Compositional Data Via Variational EM
• A Bayesian integrative approach for multi-platform genomic data: a kidney cancer case study
• Reciprocal graphical models for integrative gene regulatory network analysis
• Uncover context-specific gene regulation by transcription factors and micrornas using Bayesian sparse nonnegative factor regression
• A Bayesian model for the identification of differentially expressed genes in \textit{Daphnia magna} exposed to munition pollutants
• Bayesian nonlinear model selection for gene regulatory networks
• Identifying microRNA and gene expression networks using graph communities
• A graph Laplacian prior for Bayesian variable selection and grouping
• Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data
• Bayesian high-dimensional covariate selection in non-linear mixed-effects models using the SAEM algorithm
• Bayesian non-homogeneous hidden Markov model with variable selection for investigating drivers of seizure risk cycling
• Bayesian graphical models for differential pathways
• Exact test theory in Gaussian graphical models
• Activity of microRNAs and transcription factors in gene regulatory networks.
• A hierarchical Bayesian model for inference of copy number variants and their association to gene expression
• A loss‐based prior for Gaussian graphical models
• Incorporating grouping information in Bayesian variable selection with applications in genomics
• EMVS: the EM approach to Bayesian variable selection

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