We will compare the classification (FASN expression) we previously made based on expression levels of the FASN gene. Here, we will compare FASN high and FASN low cells to identify genes and pathways. 

Compute biomarkers

• Select the Normalized counts node and choose Compute biomarkers from the Statistics drop-down

• Choose the "FASN expression" attribute
• Do not select Split by sample
• Click Finish

This results in a Biomarkers report. 

• Double-click the Biomarkers results node to open the report

The top features are reported for the comparison. 

• Download this table with more than 10 features using the Download option 

Please click here for more information on differential analysis methods. 

Create a list 

We will create a list using List management with these 10 genes, so that we can use this list in the Gene set enrichment task. 

• Click your username in the top right corner
• Select Settings from the drop-down
• Choose Lists from the Components drop-down in the menu on the left

• Use the + New list button to add these 10 genes

• Choose Text as the list option
• Give the list a Name and Description
• Enter the 10 genes in column format as shown below
• Click Add list

Biological Interpretation 

Here we are going to perform Gene Set Enrichment on our top 10 features for the FASN high group. 

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