KEGG pathways
To aid interpretation of differential expression results, a common technique is to test for enrichment in known gene sets. The KEGG database contains curated sets of genes that are known to interact in the same biological pathway. Which KEGG pathways are over-represented in the differentially expressed genes from the leukemia study?
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The fitted model object of the leukemia study from Chapter 2, fit2, has been loaded in your workspace. The limma package is already loaded.
Extract the entrez Gene IDs from the data frame
fit2$genes.Test for enriched KEGG pathways with
kegga. Set the species to"Hs"for Homo sapiens.View the top 20 enriched KEGG pathways with
topKEGG.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Extract the entrez gene IDs
entrez <- fit2$genes[___]
# Test for enriched KEGG Pathways
enrich_kegg <- ___(fit2, geneid = entrez, species = ___)
# View the top 20 enriched KEGG pathways
___(enrich_kegg)