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Enrichment analysis: A short introduction to the core concepts of gene set enrichment analysis

A short introduction to the core concepts of enrichment analysis and its applications to bioinformatics analysis of gene lists. The presentation provides a minimal introduction to the basic idea of enrichment analysis, correction for multiple testing, importance of custom backgrounds, analysis of ranked gene lists, and applications beyond gene function. 0:00 Introduction: characterization of a gene list by finding overrepresented classes of genes 0:20 Basic idea: testing for enrichment of a single term, Gene Ontology, and systematic enrichment analysis 1:32 Multiple testing: 20 colors of jelly beans, Bonferroni correction, and false discovery rate 3:00 Custom background: the problem of using genome-wide background, 4:42 Ranked lists: mapping GO terms on a ranked gene list and significance testing 6:15 Beyond gene functions: gene set enrichment for diseases/tissues/transcription factor, kinase enrichment analysis, and organism set enrichment in microbiomes