HmmSeq: a hidden Markov model for detecting differentially expressed genes from RNA-seq data

DOI10.1214/15-AOAS815zbMATH Open1454.62323arXiv1509.04838MaRDI QIDQ746680FDOQ746680

Authors: Shiqi Cui, Subharup Guha, Marco A. R. Ferreira, Allison N. Tegge 

Publication date: 28 October 2015

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

Abstract: We introduce hmmSeq, a model-based hierarchical Bayesian technique for detecting differentially expressed genes from RNA-seq data. Our novel hmmSeq methodology uses hidden Markov models to account for potential co-expression of neighboring genes. In addition, hmmSeq employs an integrated approach to studies with technical or biological replicates, automatically adjusting for any extra-Poisson variability. Moreover, for cases when paired data are available, hmmSeq includes a paired structure between treatments that incoporates subject-specific effects. To perform parameter estimation for the hmmSeq model, we develop an efficient Markov chain Monte Carlo algorithm. Further, we develop a procedure for detection of differentially expressed genes that automatically controls false discovery rate. A simulation study shows that the hmmSeq methodology performs better than competitors in terms of receiver operating characteristic curves. Finally, the analyses of three publicly available RNA-seq data sets demonstrate the power and flexibility of the hmmSeq methodology. An R package implementing the hmmSeq framework will be submitted to CRAN upon publication of the manuscript.

Full work available at URL: https://arxiv.org/abs/1509.04838

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zbMATH Keywords

serial correlationoverdispersionBayesian hierarchical modelnext-generation sequencingfirst-order dependence

Mathematics Subject Classification ID

Bayesian inference (62F15) Markov processes: estimation; hidden Markov models (62M05) Applications of statistics to biology and medical sciences; meta analysis (62P10)

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Cited In (8)

• Identifying atypically expressed chromosome regions using RNA-Seq data
• Detection of differentially expressed genes in discrete single‐cell RNA sequencing data using a hurdle model with correlated random effects
• A Bayesian hierarchical hidden Markov model for clustering and gene selection: application to kidney cancer gene expression data
• HmmSeq
• Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes
• HmmSeq: a hidden Markov model for detecting differentially expressed genes from RNA-seq data
• Covariate-modulated large-scale multiple testing under dependence
• Title not available (Why is that?)

Uses Software

• R
• Bioconductor
• CRAN
• edgeR
• tmvtnorm
• CNAmet
• BaySeq
• DAVID

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