Gene set variation analysis

GSVA calculates gene set enrichment scores (GSVA scores) for each sample using the z-statistic matrix.
Differential expression analysis is then conducted on these GSVA scores using limma, aiming to identify differentially regulated pathways across sample groups. Finally, the differential pathway activities across sample groups are visualized using a heatmap.

z-statistic file

Output file z_statistic_table.txt from zMAP. Example file: HVP_example_z_statistic_table.txt

Sample information file

The sample information file is a three-column, tab-delimited file with the first row identifying the columns. The column names are Sample_id, Sample_condition, and MS_run. Example file: GSVA_example_sample_info.txt

Top N(number) Pathways

Extract a table of the top-ranked differentially regulated pathways across sample groups.

FDR

(BH-adjusted pvalue cutoff for significance.)