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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

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

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Please click 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

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

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• 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

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The list has been added and can now be used for further analysis. The Actions button can be used to modify this list if necessary, as shown below.

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Biological Interpretation 

Here we are going to perform Gene Set Enrichment on our top 10 features for the FASN high group that we have added as a list called "Top 10 FASN high Features". 

We need to create a list using List management with these 10 genes. 

• Go to the Analyses tab 
• Select the Normalized counts node
• Choose Gene set enrichment from the Biological interpretation drop-down in the task menu

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• Use the KEGG database for pathway enrichment
• Check Specify background gene list
• Select "Top 10 FASN high Features" as the Background gene list
• Click Finish

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This results in a Pathway enrichment report, as shown below. 

• Double-click the report to view the pathways involved in this list of genes

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Please click here for more information on Biological interpretation. 

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