Bayesian latent hierarchical model for transcriptomic meta-analysis to detect biomarkers with clustered meta-patterns of differential expression signals

DOI10.1214/18-AOAS1188MaRDI QIDQ2415465zbMATH OpenWikidataFDO

Authors Zhiguang Huo, Chi Song, George C. Tseng

Publication date 22 May 2019

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

Full work available at URL https://arxiv.org/abs/1707.03301, https://projecteuclid.org/euclid.aoas/1554861652

zbMATH Keywords

Bayesian hierarchical modelDirichlet processmeta-analysistranscriptomic differential analysis

Mathematics Subject Classification ID

Bayesian inference (62F15) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10)

Abstract: Due to the rapid development of high-throughput experimental techniques and fast-dropping prices, many transcriptomic datasets have been generated and accumulated in the public domain. Meta-analysis combining multiple transcriptomic studies can increase the statistical power to detect disease-related biomarkers. In this paper, we introduce a Bayesian latent hierarchical model to perform transcriptomic meta-analysis. This method is capable of detecting genes that are differentially expressed (DE) in only a subset of the combined studies, and the latent variables help quantify homogeneous and heterogeneous differential expression signals across studies. A tight clustering algorithm is applied to detected biomarkers to capture differential meta-patterns that are informative to guide further biological investigation. Simulations and three examples, including a microarray dataset from metabolism-related knockout mice, an RNA-seq dataset from HIV transgenic rats, and cross-platform datasets from human breast cancer, are used to demonstrate the performance of the proposed method.

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Cited in

(5)

• A Bayesian analysis strategy for cross-study translation of gene expression biomarkers
• Hypothesis setting and order statistic for robust genomic meta-analysis
• Identifying Differentially Expressed Genes in Meta-Analysis via Bayesian Model-Based Clustering
• Testing a Large Number of Composite Null Hypotheses Using Conditionally Symmetric Multidimensional Gaussian Mixtures in Genome-Wide Studies
• Meta-analysis of RNA-seq studies with an adaptive weight and truncation p-value combination test

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