1- Log in into Metabolizer. 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_example1_40_exp.txt
• Experimental design: brca_example1_40_design.txt

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

4- Press the Knockout button.

5- Press the File browser of the Expression matrix file, and select the desired file.

6- 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- All samples in your design file and design file statistics will be shown on the panel. You can search for the sample which you want to apply knockout and from the same panel you can select this sample.

8- Check the “Enable auto knockout genes” box.

9- Select Human as species.

10- In the Job information panel, press the File browser button and select the desired output folder. Give a name to the job, for example “BRCA module auto KO”.

11- Press the Launch job button. A job will be created and listed in the jobs panel. You can access this panel by clicking on the My jobs button.