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?
Este exercício faz parte do curso
Differential Expression Analysis with limma in R
Instruções do exercício
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$genes.Test for enriched KEGG pathways with
kegga. Set the species to"Hs"for Homo sapiens.View the top 20 enriched KEGG pathways with
topKEGG.
Exercício interativo prático
Experimente este exercício completando este código de exemplo.
# Extract the entrez gene IDs
entrez <- fit2$genes[___]
# Test for enriched KEGG Pathways
enrich_kegg <- ___(fit2, geneid = entrez, species = ___)
# View the top 20 enriched KEGG pathways
___(enrich_kegg)