Bayesian gene set analysis for identifying significant biological pathways

DOI10.1111/J.1467-9876.2011.00765.XMaRDI QIDQ3101562zbMATH OpenOpenAlexWikidataFDO

Authors Babak Shahbaba, Robert Tibshirani, Catherine M. Shachaf, Sylvia K. Plevritis

Publication date 29 November 2011

Published in Journal of the Royal Statistical Society Series C: Applied Statistics (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc3156489

zbMATH Keywords

hierarchical Bayesian modelsmixture priors

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50)

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Cites work

• Group additive regression models for genomic data analysis
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
• On testing the significance of sets of genes
• Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis
• Slice sampling. (With discussions and rejoinder)
• Spike and Slab Gene Selection for Multigroup Microarray Data
• The Calculation of Posterior Distributions by Data Augmentation

Cited in

(12)

• Statistical inference for high-dimensional pathway analysis with multiple responses
• Biological pathway selection through Bayesian integrative modeling
• Graphical modeling for gene set analysis: a critical appraisal
• Smoothing gene expression data with network information improves consistency of regulated genes
• Corridendum: ``Biological pathway selection through Bayesian integrative modeling
• Logistic regression augmented community detection for network data with application in identifying autism-related gene pathways
• Defining a robust biological prior from pathway analysis to drive network inference
• Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data
• Bayesian functional enrichment analysis for the Reactome database
• Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes
• Bayesian nonparametric variable selection as an exploratory tool for discovering differentially expressed genes
• Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis

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