Make comparisons using Compute biomarkers and Biological interpretation

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

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.

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".

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