Once we have performed GSA DESeq2 to identify differentially expressed genes, we can create a list of significantly differentially expressed genes using cutoff thresholds. 

...

The task report spreadsheet will open showing genes on rows and the results of the GSA DESeq2 on columns (Figure 1).

To get a sense of what filtering thresholds to set, we can view a volcano plot for a comparison. 

...

Thresholds for the cutoff lines are set using the Significance card Statistics card (Configuration panel > Content Configure > SignificanceStatistics). The default thresholds are |2| for the X axis and 0.05 for the Y axis. 

• Switch to the browser tab showing the GSA DESeq2 report
• Click FDR step up
• Click the triangle next to FDR step up to open the FDR step up options
• Leave All contrasts selected
• Set the cutoff value to 0.05. Hit Enter.

...

Note that the number of genes that pass the filter is listed at the top of the filter menu next to Results: and will update to reflect any changes to the filter. Here, 32 27 genes pass the filter (Figure 3). Depending on your settings, the number may be slightly different.

...

• Click  to create a data node with only the genes that pass the filter

...

...