Bayesian Pathway Enrichment Analysis
Bayesian pathway enrichment analysis tests whether a predefined set of genes — a biological pathway — is systematically overrepresented among genes that show evidence of differential activity in an experiment. Unlike classical over-representation tests, it encodes prior biological knowledge as a prior distribution and updates it with the observed expression data, yielding posterior probabilities of enrichment rather than p-values. This probabilistic framing naturally handles small samples, multiple pathways, and uncertainty propagation in a coherent statistical framework.
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- Baldi, P., & Long, A. D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics, 17(6), 509–519. · DOI 10.1093/bioinformatics/17.6.509
- Newton, M. A., Quintana, F. A., Den Boon, J. A., Bhattacharya, S., & Ahlquist, P. (2004). Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. The Annals of Applied Statistics, 1(1), 85–106. · URL
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