DATA:

We have a set of breast cancer patients and a set of healthy samples. We want to know which functions are involved in the development of the disease. For that, we have performed a differential expression between both groups, and selected the top 50 genes, that is, the 50 genes which are upregulated in patients with breast cancer and have lowest adjusted p.value.

List of genes: brca_diffexp_toplist50.txt

We are going to use Single enrichment to look for the functional profile.

EXERCISE:

1. Go to Functional → Single Enrichment FatiGO
2. Define comparison as Id List vs. rest of genome
3. Set the list of genes above
4. Set “Remove from list2 those appearing in list1”
5. Select Human
6. Check the databases you are interested in (all for example)
7. Launch job

QUESTIONS:

1. How many significant results are there? In which databases?
2. Which is the most significant term in
3. Which relation do the terms have with the disease under study?