The collection of pathways/gene sets utilized in i-GSEA4GWAS are extracted and curated from MSigDB v2.5 (http://www.broadinstitute.org/gsea/msigdb/) (15) to ensure comprehensiveness and high quality. It includes gene sets denoting canonical pathways integrated from a variety of online resources like KEGG (19) and BioCarta (http://www.biocarta.com/), and GO (gene ontology) terms with high confidence (20). Additionally, i-GSEA4GWAS supports customized gene sets, i.e. users can upload their own gene sets. This provides the opportunity that the knowledge database (gene sets) can always be expanded, and makes it easy for users to test their hypothesis within their research interest.
