A Bayesian graphical modeling approach to microRNA regulatory network inference
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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.
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Cites work
- A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
- A stochastic partitioning method to associate high-dimensional responses and covariates
- Bayesian Variable Selection in Multinomial Probit Models to Identify Molecular Signatures of Disease Stage
- Detecting differential gene expression with a semiparametric hierarchical mixture method
- Multivariate Bayesian Variable Selection and Prediction
- Probabilistic Networks and Expert Systems
- Some matrix-variate distribution theory: Notational considerations and a Bayesian application
Cited in
(30)- A Bayesian integrative approach for multi-platform genomic data: a kidney cancer case study
- Bayesian Lesion Estimation with a Structured Spike-and-Slab Prior
- A hierarchical Bayesian model for inference of copy number variants and their association to gene expression
- Bayesian nonlinear model selection for gene regulatory networks
- Sparse inverse covariance estimation for high-throughput microRNA sequencing data in the Poisson log-normal graphical model
- Identifying microRNA and gene expression networks using graph communities
- 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
- miRNA-target gene regulatory networks: a Bayesian integrative approach to biomarker selection with application to kidney cancer
- A Bayesian model for the identification of differentially expressed genes in \textit{Daphnia magna} exposed to munition pollutants
- A graph Laplacian prior for Bayesian variable selection and grouping
- Reciprocal graphical models for integrative gene regulatory network analysis
- Hierarchical normalized completely random measures for robust graphical modeling
- Bayesian approaches for large biological networks
- Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data
- Incorporating grouping information in Bayesian variable selection with applications in genomics
- A loss‐based prior for Gaussian graphical models
- Bayesian graphical models for differential pathways
- Bayesian learning of multiple directed networks from observational data
- Response variable selection in multivariate linear regression
- EMVS: the EM approach to Bayesian variable selection
- A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes
- scientific article; zbMATH DE number 6275385 (Why is no real title available?)
- Uncover context-specific gene regulation by transcription factors and micrornas using Bayesian sparse nonnegative factor regression
- A novel Bayesian multiple testing approach to deregulated miRNA discovery harnessing positional clustering
- Exact test theory in Gaussian graphical models
- Bayesian graphical models for modern biological applications
- Activity of microRNAs and transcription factors in gene regulatory networks.
- MicroRNA Regulatory Network: Structure and Function
- Latent Network Estimation and Variable Selection for Compositional Data Via Variational EM
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