Detecting differential gene expression with a semiparametric hierarchical mixture method

DOI10.1093/BIOSTATISTICS/5.2.155zbMATH Open1096.62124OpenAlexW2170264612WikidataQ47850306 ScholiaQ47850306MaRDI QIDQ5701280FDOQ5701280

Authors: Michael A. Newton, Amine Noueiry, Deepayan Sarkar, Paul Ahlquist 

Publication date: 2 November 2005

Published in: Biostatistics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1093/biostatistics/5.2.155

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zbMATH Keywords

MicroarraysEmpirical BayesStatistical analysisPosterior probabilityFalse discovery rateOrdered alternatives

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

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• Microarrays, empirical Bayes and the two-groups model
• Fully Bayesian mixture model for differential gene expression: simulations and model checks
• Estimating the Proportion of True Null Hypotheses, with application to DNA Microarray Data
• Cluster analysis using multivariate normal mixture models to detect differential gene expression with microarray data
• An empirical Bayes mixture method for effect size and false discovery rate estimation
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• Bayesian Analysis of Mass Spectrometry Proteomic Data Using Wavelet-Based Functional Mixed Models
• Multiple testing on standardized mortality ratios: a Bayesian hierarchical model for FDR estimation
• Bayesian ranking and selection methods using hierarchical mixture models in microarray studies
• Detecting Differential Expressions in GeneChip Microarray Studies
• Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes
• Vladimir Steklov: a mathematician at the turn of the era
• Statistics of mixtures with varying concentrations with application to DNA microarray data analysis
• The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data
• A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes
• Efficient Bayesian regularization for graphical model selection
• Bayesian inference and testing of group differences in brain networks
• A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
• Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles
• A general framework for multiple testing dependence
• Multiple hypothesis testing and clustering with mixtures of non-central \(t\)-distributions applied in microarray data analysis
• Generalized species sampling priors with latent beta reinforcements
• Flexible temporal expression profile modelling using the Gaussian process
• A mixture modeling framework for differential analysis of high-throughput data
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• A hierarchical semiparametric model for incorporating intergene information for analysis of genomic data
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• Reciprocal graphical models for integrative gene regulatory network analysis
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• Estimating effect sizes of differentially expressed genes for power and sample-size assessments in microarray experiments
• A Bayesian Mixture Model for Differential Gene Expression
• Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples
• A three component latent class model for robust semiparametric gene discovery
• Bayesian Modeling of Differential Gene Expression
• Spiked Dirichlet process priors for Gaussian process models
• An Integrative Bayesian Modeling Approach to Imaging Genetics
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• A new approach to multiple testing of grouped hypotheses
• Bayesian Genome- and Epigenome-Wide Association Studies with Gene Level Dependence
• A Flexible and Powerful Bayesian Hierarchical Model for ChIP-Chip Experiments
• A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
• Unsupervised empirical Bayesian multiple testing with external covariates
• Modeling Microarray Data Using a Threshold Mixture Model
• Limit theorems for hybridization reactions on oligonucleotide microarrays
• A heavy-tailed empirical Bayes method for replicated microarray data
• A new class of mixture models for differential gene expression in DNA microarray data
• Bayesian testing of many hypotheses \(\times \) many genes: a study of sleep apnea
• Mixture Model on the Variance for the Differential Analysis of Gene Expression Data
• A statistical analysis of memory CD8 T cell differentiation: An application of a hierarchical state space model to a short time course microarray experiment
• Covariate adjusted differential variability analysis of DNA methylation with propensity score method
• Bayesian sparse graphical models for classification with application to protein expression data
• HmmSeq: a hidden Markov model for detecting differentially expressed genes from RNA-seq data
• Gaga: a parsimonious and flexible model for differential expression analysis
• Selecting massive variables using an iterated conditional modes/medians algorithm
• A time-series DDP for functional proteomics profiles
• Nonparametric analysis of replicated microarray experiments
• Bayesian Error‐in‐Variable Survival Model for the Analysis of GeneChip Arrays
• Statistical Methods for Expression Quantitative Trait Loci (eQTL) Mapping
• Bayesian decision theoretic multiple comparison procedures: an application to phage display data
• Wavelet Thresholding with Bayesian False Discovery Rate Control
• An empirical Bayes optimal discovery procedure based on semiparametric hierarchical mixture models
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• Batch effects correction with unknown subtypes
• A Bayesian graphical modeling approach to microRNA regulatory network inference
• A mixture model approach for the analysis of microarray gene expression data.
• A hierarchical Bayesian model for inference of copy number variants and their association to gene expression
• A Laplace mixture model for identification of differential expression in microarray experiments
• A statistical framework for testing functional categories in microarray data
• A loss‐based prior for Gaussian graphical models
• Assessing Differential Gene Expression with Small Sample Sizes in Oligonucleotide Arrays Using a Mean‐Variance Model
• Extracting gene regulation information for cancer classification
• A Bayesian approach for estimating dynamic functional network connectivity in fMRI data
• Multiple testing in genome-wide association studies via hierarchical hidden Markov models
• Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP
• Spatially dependent multiple testing under model misspecification, with application to detection of anthropogenic influence on extreme climate events
• Bayesian Structure Learning in Multilayered Genomic Networks
• Spectral clustering via sparse graph structure learning with application to proteomic signaling networks in cancer
• A two-stage empirical Bayes method for identifying differentially expressed genes
• A mixture model approach for the analysis of small exploratory microarray experiments
• A robust unified approach to analyzing methylation and gene expression data
• On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data
• A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data
• Exploiting blank spots for model-based background correction in discovering genes with DNA array data
• Detection of differentially expressed genes in discrete single‐cell RNA sequencing data using a hurdle model with correlated random effects
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• Distributed eQTL analysis with auxiliary information
• Supporting informationa robust method for large-scale multiple hypotheses testing

Uses Software

• R
• EBarrays

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