The methods used for enrichment analysis vary across different tools. g:Profiler, likewise to Enrichr and WebGestalt (1,2), provides the most widely used over-representation analysis approach that uses the hypergeometric test to measure the significance of functional term in the input gene list. There exist tools that provide other methods that also take into account additional ranking information of gene lists (WebGestalt, GSEA (2,9)) or use prior knowledge from gene regulation networks (WebGestalt (2)). All of these methods have their own limitations and there are no good benchmark data to assess and compare different methods (14). In order to serve the users an easy-to-use and fast enrichment tool, g:Profiler has been focusing on one approach only.
