A Bayesian nonparametric mixture model for selecting genes and gene subnetworks
From MaRDI portal
(Redirected from Publication:400643)
Abstract: It is very challenging to select informative features from tens of thousands of measured features in high-throughput data analysis. Recently, several parametric/regression models have been developed utilizing the gene network information to select genes or pathways strongly associated with a clinical/biological outcome. Alternatively, in this paper, we propose a nonparametric Bayesian model for gene selection incorporating network information. In addition to identifying genes that have a strong association with a clinical outcome, our model can select genes with particular expressional behavior, in which case the regression models are not directly applicable. We show that our proposed model is equivalent to an infinity mixture model for which we develop a posterior computation algorithm based on Markov chain Monte Carlo (MCMC) methods. We also propose two fast computing algorithms that approximate the posterior simulation with good accuracy but relatively low computational cost. We illustrate our methods on simulation studies and the analysis of Spellman yeast cell cycle microarray data.
Recommendations
- Bayesian nonlinear model selection for gene regulatory networks
- A Bayesian Mixture Model for Differential Gene Expression
- A Bayesian approach to nonlinear probit gene selection and classification
- scientific article; zbMATH DE number 1950552
- Bayesian Models for Gene Expression With DNA Microarray Data
Cites work
- A Bayesian Mixture Model for Differential Gene Expression
- A Bayesian nonparametric mixture model for selecting genes and gene subnetworks
- A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
- A hierarchical semiparametric model for incorporating intergene information for analysis of genomic data
- Bayesian Density Estimation and Inference Using Mixtures
- Bayesian joint modeling of multiple gene networks and diverse genomic data to identify target genes of a transcription factor
- Bayesian variable selection in structured high-dimensional covariate spaces with applications in genomics
- Correlated \(z\)-values and the accuracy of large-scale statistical estimates
- Detecting novel associations in large data sets
- Emergence of Scaling in Random Networks
- Estimating Normal Means with a Dirichlet Process Prior
- Gibbs Sampling Methods for Stick-Breaking Priors
- Incorporating Predictor Network in Penalized Regression with Application to Microarray Data
- Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes
- Large-Scale Simultaneous Hypothesis Testing
- Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems
- More power via graph-structured tests for differential expression of gene networks
- Nonparametric Bayesian Estimation of Positive False Discovery Rates
- Nonparametric Bayesian data analysis
- Tests for independence in nonparametric regression
Cited in
(11)- A Bayesian nonparametric mixture model for selecting genes and gene subnetworks
- Bayesian neural networks for selection of drug sensitive genes
- NetMix: a network-structured mixture model for reduced-bias estimation of altered subnetworks
- Gene prediction using multinomial probit regression with Bayesian gene selection
- Feature selection and classification over the network with missing node observations
- Bayesian nonlinear model selection for gene regulatory networks
- Variable selection for BART: an application to gene regulation
- Molecular multiplex network inference using Gaussian mixture hidden Markov models
- scientific article; zbMATH DE number 5347341 (Why is no real title available?)
- A spatial Bayesian semiparametric mixture model for positive definite matrices with applications in diffusion tensor imaging
- Variable Selection in Regression Mixture Modeling for the Discovery of Gene Regulatory Networks
This page was built for publication: A Bayesian nonparametric mixture model for selecting genes and gene subnetworks
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q400643)
