Blue and Beige Purely Typographic Church Logo (6)

Enrichment Analysis

Over Representation Analysis (ORA)

Pathway analysis includes any type of  techniques that uses known sets of genes which are related or coordinated in their expression to interpret. ORA only requires a list of gene IDs (no stats needed), unlike GSEA which needs gene-level summary statistics. It is a simple and inexpensive method, however, it needs an arbitrary threshold, ignores the associated statistics and assumes there is an independence of genes and pathways. 

Gene set enrichment analysis (GSEA)

This is a method to find out the classes of either genes or proteins which are over-represented in the sample. It employs statistical approaches to pinpoint enriched or depleted groups of genes. This includes Gene Ontology (GO) analysis, which uses defined classes to describe gene function. Functions are grouped into 3 aspects: Molecular Function, Cellular Component, Biological Process. GSEA also includes Kyoto Encyclopedia of genes and genome (KEGG) analysis. KEGG is a database of pathways which map molecular interactions and reaction networks. Including a range of biochemical processes, divided into the following groups: 

  1. Metabolism
  2. Genetic information processing
  3. Environmental information processing
  4. Cellular processes
  5. Organismal systems
  6. Human diseases
  7. Drug development.