Functional enrichment analysis
Reimand, Jüri, Ruth Isserlin, Veronique Voisin, Mike Kucera, Christian Tannus-Lopes, Asha Rostamianfar, Lina Wadi, et al. “Pathway Enrichment Analysis and Visualization of Omics Data Using g:Profiler, GSEA, Cytoscape and EnrichmentMap.” Nature Protocols, January 21, 2019 - Pathway enrichment analysis tutorial. Main tools - g:Profiler, GSEA, Cytoscape, EnrichmentMap. Definitions, step-by-step protocol.
Bard, Jonathan B. L., and Seung Y. Rhee. “Ontologies in Biology: Design, Applications and Future Challenges.” Nature Reviews. Genetics, (March 2004) - Ontologies review
Ackermann, Marit, and Korbinian Strimmer. “A General Modular Framework for Gene Set Enrichment Analysis.” BMC Bioinformatics, (2009) - All steps for enrichment analysis, methods, statistics, GSEA.
Efron, Bradley, and Robert Tibshirani. “On Testing the Significance of Sets of Genes.” The Annals of Applied Statistics, 2007 - maxmean statistics for enrichment analysis. Comparison with GSEA.
Huang, Da Wei, Brad T. Sherman, and Richard A. Lempicki. “Bioinformatics Enrichment Tools: Paths toward the Comprehensive Functional Analysis of Large Gene Lists.” Nucleic Acids Research, (January 2009) - Gene enrichment analyses tools. Statistics, concept of background. 68 tools, table
Hung, Jui-Hung, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, and Charles DeLisi. “Gene Set Enrichment Analysis: Performance Evaluation and Usage Guidelines.” Briefings in Bioinformatics, (May 2012) - Details of GSEA. Statistics, correction for multiple testing. Lack of gold standard - concept of mutual coverage.
Khatri, Purvesh, Marina Sirota, and Atul J. Butte. “Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges.” PLoS Computational Biology, (2012) - Review of enrichment analyses techniques, focus on pathways, Table 1 lists tools, limitations.
Hänzelmann, Sonja, Robert Castelo, and Justin Guinney. “GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data.” BMC Bioinformatics (January 16, 2013) - GSVA - a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner
Khatri, Purvesh, Marina Sirota, and Atul J. Butte. “Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges.” PLoS Computational Biology, (February 23, 2012) - Overview of pathway analysis methods (ORA - over-representation analysis, FCS - functional class scoring, PT - pathway topology) and tools. Methods, limitations.
Nam D., and Seon-Young K.. “Gene-Set Approach for Expression Pattern Analysis.” Briefings in Bioinformatics 2008
Mutation Consequences and Pathway Analysis working group. “Pathway and Network Analysis of Cancer Genomes.” Nature Methods 2015
de Leeuw, C. et.al. “The Statistical Properties of Gene-Set Analysis.” Nature Reviews 2016