Gene ontology categories

In the previous exercise, you tested for enrichment of biological pathways. Now you will test for enrichment in gene sets that are known to influence the same biological process, known as gene ontology (GO) categories. Which GO categories 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

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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 GO categories with goana. Set the species to "Hs" for Homo sapiens.
View the top 20 enriched GO categories with topGO. Set the argument ontology to "BP" to return Biological Processes.

Hands-on interactive exercise

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

# Extract the entrez gene IDs
entrez <- ___

# Test for enriched GO categories
enrich_go <- ___(fit2[1:500, ], geneid = ___, species = ___)

# View the top 20 enriched GO Biological Processes
___(enrich_go, ontology = ___)

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