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  3. Differential Expression Analysis with limma in R

Exercise

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?

Instructions

100 XP

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.