The first example data is SNP P-value from the GWAS of HIV-1 host control investigation, which studied the quantitative trait—HIV-1 viral load set point and used Illumina HumanHap550 BeadChip (24). The input includes 518 754 SNPs with corresponding P-values. There are 479 086 SNPs mapped to 16 524 genes by using the default ‘500 kb upstream and downstream of gene’. 251 gene sets were selected by using ‘canonical pathways’, and using the default gene set size ranges from 20 through 200. A total of 23 pathways/gene sets were identified to be possibly correlated with the trait (FDR < 0.25). Among the 23 pathways, five pathways namely ‘antigen processing and presentation’, ‘inflampathway’, ‘cskpathway’, ‘ribosome’ and ‘st myocyte ad pathway’ have high confidence (FDR < 0.05). The pathways ‘antigen processing and presentation’ (FDR = 0.009), ‘inflampathway’ (FDR = 0.010), and ‘cskpathway’ (FDR = 0.011) have been replicated in our follow-up work of the initial GWAS by either the top hits or using GSEA (9). Both the pathways ‘ribosome’ and ‘st myocyte ad pathway’ were only identified by i-GSEA (FDR < 0.05) and
