Worked example Differential signaling

:https://www.youtube.com/watch?v=ytyagfQpQPk&feature=youtu.be

1- Log in into HiPathia. For further information on this step visit Logging in.

2- We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix and the experimental design from these links:

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

3- Upload the data to HiPathia in the data panel by clicking on My data. For further information on this step visit Upload your data.

4- Press the Differential signaling button.

5- In the Input data panel. Press the File browser of the Expression matrix file, and select the desired file.

6- In the Design data panel select Two group comparison. Press the File browser of the Experimental design file, and select the desired file. Automatically Condition 1 and Condition 2 files are selected. Change Condition 1 to “Tumor” and Condition 2 to “Normal”.

7- Select Human as species (by default).

8- In the Function level analysis, check both checkboxes, Gene ontology and Uniprot keywords.

9- In the Pathways panel select all the pathways (by default).

10- In the Study information panel, press the File browser button and select the desired output folder. In this case we will use analysis_BRCA. Give a name to the study, for example “BRCA Differential signaling”.

11- Press the Run analysis button. A study will be created and listed in the studies panel. You can access this panel by clicking on the My studies button.