Table 4.

Integrative Analysis.

	App Function	Description
IA1	Scatter Plot Comparison	User input features are merged and plotted Samples are colored based on metadata type
IA2	Correlation Rank Plot	Assessing the relationship between ssGSEA score and gene expression performed Correlation can be performed as Spearman, Pearson, or Kendall Correlation values plotted by rank from lowest to highest
IA3	Matrix Comparison File Upload	Upload two expression matrices and two metadata files
IA4	Log2FC Comparison Scatter Plot	Differential gene expression analysis with LIMMA performed on both matrices Log2 fold change values subset and difference between matrices calculated Expression data displayed as scatter plot
IA5	Reciprocal GSEA	Differential gene expression analysis with LIMMA Four gene sets derived differentially expressed genes (two upregulated, and two downregulated gene set) GSEA performed on the reciprocal data
IA6	Reciprocal ssGSEA	Differential gene expression analysis with LIMMA Four gene sets derived differentially expressed genes (two upregulated, and two downregulated gene set) ssGSEA performed on the reciprocal data
IA7	Venn Diagram	Differential gene expression analysis with LIMMA Overlapping differentially expressed genes Perform Fisher’s exact test. Calculate Cohen’s kappa, and Jaccard index to compare between the two matrix and across user selected pathways.