i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study

Zhang, Kunlin; Cui, Sijia; Chang, Suhua; Zhang, Liuyan; Wang, Jing

There are always conflicts between the amount and the quality of the gene sets utilized for computation. Using a large amount of gene sets, such as all GO terms, will introduce large background and noise due to the large number and low confidence of some gene sets, while only using a few gene sets will lose information. Moreover, the knowledge of gene sets is keeping increasing. To overcome this, we chose a balanced strategy, using a curated pathway/gene set database with consideration of both comprehensiveness and high quality, and allow researchers to upload their customized gene sets to make sure the gene sets of research focus will be well represented. This ensures that i-GSEA4GWAS contains a high-quality and reasonable search space. The i-GSEA4GWAS will be regularly updated to ensure the most up-to-date searching database and annotations. i-GSEA4GWAS also integrates the curated copy number variations (CNVs) from the Database of Genomic Variants (http://projects.tcag.ca/variation/) (34) . In the future, the CNV functional module will be further extended to include the CNV probes of Illumina, Affymetrix and more genome-wide genotyping arrays.