A hidden Markov model approach to testing multiple hypotheses on a tree-transformed gene ontology graph

DOI10.1198/JASA.2010.TM10195MaRDI QIDQ5255685zbMATH OpenOpenAlexFDO

Authors Kun Liang, Dan Nettleton

Publication date 17 June 2015

Published in Journal of the American Statistical Association (Search for Journal in Brave)

Full work available at URL https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1094&context=stat_las_preprints

zbMATH Keywords

false discovery ratemultiple testingdifferential expressionmicroarrayBayesian data analysisgene set enrichment analysisdirect acyclic graph

Mathematics Subject Classification ID

Bayesian inference (62F15) Diagnostics, and linear inference and regression (62J20) Applications of statistics to biology and medical sciences; meta analysis (62P10) Graphical methods in statistics (62A09) Paired and multiple comparisons; multiple testing (62J15)

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(10)

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• Adaptive filtering increases power to detect differentially expressed genes
• Variable importance assessments and backward variable selection for multi-sample problems
• A hierarchical semiparametric model for incorporating intergene information for analysis of genomic data
• Combined hypothesis testing on graphs with applications to gene set enrichment analysis
• TreeHugger: a new test for enrichment of gene ontology terms
• False discovery rate estimation for large-scale homogeneous discrete \(p\)-values
• Covariate-adjusted multiple testing in genome-wide association studies via factorial hidden Markov models
• Bayesian hidden Markov models for dependent large-scale multiple testing
• Variational Bayesian inference for association over phylogenetic trees for microorganisms

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