Identifying atypically expressed chromosome regions using RNA-Seq data

DOI10.1007/S10260-019-00496-4MaRDI QIDQ2220294zbMATH OpenOpenAlexWikidataFDO

Authors Vinícius Diniz Mayrink, Flávio B. Gonçalves

Publication date 22 January 2021

Published in Statistical Methods and Applications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1708.05895

zbMATH Keywords

Bayesian inferencecancergene expressionGibbs samplingmixture model

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Abstract: The number of studies dealing with RNA-Seq data analysis has experienced a fast increase in the past years making this type of gene expression a strong competitor to the DNA microarrays. This paper proposes a Bayesian model to detect down and up-regulated chromosome regions using RNA-Seq data. The methodology is based on a recent work developed to detect up-regulated regions in the context of microarray data. A hidden Markov model is developed by considering a mixture of Gaussian distributions with ordered means in a way that first and last mixture components are supposed to accommodate the under and overexpressed genes, respectively. The model is flexible enough to efficiently deal with the highly irregular spaced configuration of the data by assuming a hierarchical Markov dependence structure. The analysis of four cancer data sets (breast, lung, ovarian and uterus) is presented. Results indicate that the proposed model is selective in determining the regulation status, robust with respect to prior specifications and provides tools for a global or local search of under and overexpressed chromosome regions.

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Cites work

• A Bayesian Mixture Model for Differential Gene Expression
• Fully Bayesian mixture model for differential gene expression: simulations and model checks
• NOTES ON CONTINUOUS STOCHASTIC PHENOMENA
• Removing technical variability in RNA-seq data using conditional quantile normalization
• Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
• The Collapsed Gibbs Sampler in Bayesian Computations with Applications to a Gene Regulation Problem

Cited in

(2)

• Comparing segmentation methods for genome annotation based on RNA-seq data
• HmmSeq: a hidden Markov model for detecting differentially expressed genes from RNA-seq data

Describes a project that uses

Uses Software

• edgeR
• R
• Bioconductor
• maSigPro
• CODA
• DEseq
• PLNseq

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