GSA-Genie: a web application for gene set analysis

Abstract

Gene set analysis is often used to interpret results from upstream analysis through predefined gene sets that are linked to biological features such as cell cycle or tumorgenesis. Gene sets have been defined in the literature via various criteria and are archived by numerous databases. We compiled over 2.3 million gene sets from 17 sources, and made them accessible through a web application, GSA-Genie. Selected gene sets can be analyzed online using one of 16 statistical methods. These methods can be grouped into two strategies: test of gene set over-representation within a gene list, or comparison of a gene-level statistics between gene set and background. GSA-Genie operates on a Shiny web server, hosted in a cloud instance within Amazon Web Services. GSA-Genie offers a broad selection of gene sets and statistical methods comparing to existing tools. GSA-Genie is freely available at http://gsagenie.awsomics.org.