Table 3.

Gene Set Enrichment Analysis Module.

	App Function	Description
GA1	Enrichment Plot	User selects comparison groups Signal-to-noise ranking performed on expression data GSEA function performed with chosen gene set
GA2	Gene Expression Heatmap	User selects comparison groups Signal-to-noise ranking performed on expression data GSEA function performed with chosen gene set Expression data log2 transformed and scaled Genes from chosen gene set displayed in the heatmap
GA3	GSEA Summary Table	Displays user pre-generated enriched signatures table
GA4	Generate Summary Table	GSEA function performed on expression data with user input GMT file Enriched signatures table produced is displayed
GA5	ssGSEA Boxplots	User-selects gene set and single-sample GSEA method Comparing groups for statistical differences