Process / pipelineBioinformatics / omics
Gene Set Enrichment Analysis (GSEA)
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether a predefined set of genes — representing a biological pathway, process, or function — shows statistically significant, coordinated differences between two biological conditions. Unlike simple fold-change filtering, GSEA operates on all measured genes ranked by a correlation metric, detecting subtle but consistent shifts across an entire pathway even when no single gene passes a significance threshold.
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Sources
- Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545–15550. DOI: 10.1073/pnas.0506580102 ↗
- Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E., Houstis, N., Daly, M. J., Patterson, N., Mesirov, J. P., Golub, T. R., Tamayo, P., Spiegelman, B., Lander, E. S., Hirschhorn, J. N., Altshuler, D., & Groop, L. C. (2003). PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nature Genetics, 34(3), 267–273. DOI: 10.1038/ng1180 ↗
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Bayesian Gene Set Enrichment AnalysisBayesian Microbiome Diversity AnalysisBayesian Pathway Enrichment AnalysisBayesian RNA-seq differential expressionDifferential ChIP-seq peak callingDifferential pathway enrichment analysiseQTL AnalysisMachine learning-assisted gene set enrichment analysisMachine learning-assisted pathway enrichment analysisMachine learning-assisted RNA-seq differential expressionMachine learning-assisted single-cell RNA-seq analysisMetabolomics analysisMulti-omics gene set enrichment analysisMulti-omics metabolomics analysisMulti-omics microbiome diversity analysisMulti-omics Pathway Enrichment AnalysisMulti-omics proteomics analysisMulti-omics RNA-seq differential expressionMulti-omics single-cell RNA-seq analysisNetwork-based copy number variation analysisNetwork-based gene set enrichment analysisNetwork-based GWASNetwork-based metabolomics analysisNetwork-based microbiome diversity analysisNetwork-based pathway enrichment analysisNetwork-based RNA-seq differential expressionNetwork-based single-cell RNA-seq analysisPathway Enrichment AnalysisProteomics AnalysisRNA-seq Differential ExpressionSingle-cell Gene Set Enrichment AnalysisSingle-cell RNA-seq analysisSingle-cell RNA-seq differential expressionTime-series gene set enrichment analysisTime-series pathway enrichment analysisTime-series RNA-seq differential expressionTime-series single-cell RNA-seq analysis