The pathways/gene sets, with FDR < 0.25 (the threshold of FDR < 0.25 denotes the confidence of ‘possible’ or ‘hypothesis’, while the threshold of FDR < 0.05 is regarded as ‘high confidence’ or ‘with statistical significance’), are displayed in a tabular form with links to detailed text information of pathways/gene sets, genes and SNPs. One characteristic feature of i-GSEA4GWAS output is the Manhattan plot of gene set, which uses the Manhattan plot of GWAS as background, and highlights the results of association test for a given pathway/gene set. It helps users to compare the association results of the given pathway/gene set with the genome-scale data graphically. The result page also contains the download URL, from where all the results, both texts and figures, can be downloaded.
