EGAN: exploratory gene association networks

Abstract

Summary: Exploratory Gene Association Networks (EGAN) is a Java desktop application that provides a point-and-click environment for contextual graph visualization of high-throughput assay results. By loading the entire network of genes, pathways, interactions, annotation terms and literature references directly into memory, EGAN allows a biologist to repeatedly query and interpret multiple experimental results without incurring additional delays for data download/integration. Other compelling features of EGAN include: support for diverse -omics technologies, a simple and interactive graph display, sortable/searchable data tables, links to external web resources including ≥240 000 articles at PubMed, hypergeometric and GSEA-like enrichment statistics, pipeline-compatible automation via scripting and the ability to completely customize and/or supplement the network with new/proprietary data. Availability: Runs on most operating systems via Java; downloadable from http://akt.ucsf.edu/EGAN/ Contact:jesse.paquette@cc.ucsf.edu Supplementary information: Supplementary data are available at Bioinformatics online.