Lecture 7: Gene Set/Pathway Enrichment Analysis (07/08/2024)

↩︎️ Lecture Schedule


What we will learn

Gene Set Enrichment Analysis (GSEA)

  • Analyzing changes in biological pathways using NGS (RNA-seq) data provides a good understanding of global differences across biological conditions

  • Different methods for analyzing gene set changes such as over-representation /enrichment exist (technically different, but generally lead to similar results)

Pathway Databases & fgsea package

  • Online resources provide biological pathway definition & analysis tools

  • fgsea & msigdbr packages provide a good framework for such analysis in R

What we will Practice

Using the Practical DESeq2 results from [Lecture 6] the publicly-available RNA seq data (see overview here), we will perform each step in the gene set enrichment analysis.