Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes

DOI10.1007/S13253-015-0232-3MaRDI QIDQ906080zbMATH OpenOpenAlexWikidataFDO

Authors Andrew Lithio, Dan Nettleton

Publication date 29 January 2016

Published in Journal of Agricultural, Biological and Environmental Statistics (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc4841633

zbMATH Keywords

geneticsempirical Bayessplit-plotintegrated nested Laplace approximationShrinkBayes

Mathematics Subject Classification ID

Bayesian inference (62F15) Generalized linear models (logistic models) (62J12) Applications of statistics to environmental and related topics (62P12) Protein sequences, DNA sequences (92D20) Empirical decision procedures; empirical Bayes procedures (62C12)

Recommendations

• Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis
• A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
• Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
• Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates
• Contrastive latent variable modeling with application to case-control sequencing experiments

Cites work

• Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations (with discussion)
• DESeq2
• Fully Bayesian mixture model for differential gene expression: simulations and model checks
• Multiple testing on standardized mortality ratios: a Bayesian hierarchical model for FDR estimation
• Statistical analysis of next generation sequencing data
• The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data

Cited in

(3)

• Fully Bayesian analysis of allele-specific RNA-seq data
• Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis
• Estimation and testing of gene expression heterosis

Describes a project that uses

Uses Software

• DESeq2
• Voom
• ShrinkBayes
• limma
• DEseq
• BaySeq
• edgeR
• gcrma
• Bioconductor

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