Pathway enrichment

To better understand the effect of the differentially expressed genes in the doxorubicin study, you will test for enrichment of known biological pathways curated in the KEGG database. Which KEGG pathways are over-represented in the differentially expressed genes for the contrasts "dox_wt" and "interaction"?

This exercise is part of the course

Differential Expression Analysis with limma in R

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Exercise instructions

The fitted model object 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 for the contrast "dox_wt". Set the species to "Mm" for Mus musculus.
View the top 5 enriched KEGG pathways with topKEGG.
Repeat the pathway enrichment for the contrast "interaction".

Hands-on interactive exercise

Have a go at this exercise by completing this sample code.

# Extract the entrez gene IDs
entrez <- ___

# Test for enriched KEGG Pathways for contrast dox_wt
enrich_dox_wt <- ___(fit2, coef = ___, geneid = entrez, species = ___)

# View the top 5 enriched KEGG pathways
___(enrich_dox_wt, number = 5)

# Test for enriched KEGG Pathways for contrast interaction
enrich_interaction <- ___(fit2, coef = ___, geneid = ___, species = ___)

# View the top 5 enriched KEGG pathways
___(___, number = ___)

Edit and Run Code