Differential signaling exercises

In this page you will find different exercises for further practising in the use of the HiPathia Prediction tool. Try to answer the questions using the results given by HiPathia for each case.

To see how to use the application please visit the documentation of the prediction tool or the Differential Signaling worked example.

We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. There are different subtypes of Breast Cancer. In this exercise we will compare two kinds of breast cancer subtypes.

First we will analyze the basal subtype, also called triple negative, with healthy breast tissue. You can download the normalized expression matrix and the experimental design from these links:

• Expression matrix: brca_genes_vals_bn.txt
• Experimental design: brca_normal-basal_ed.txt