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Bioinformatics. 2010 Jan 15;26(2):285-6. doi: 10.1093/bioinformatics/btp656. Epub 2009 Nov 23.

EGAN: exploratory gene association networks.

Author information

  • 1Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA. jesse.paquette@cc.ucsf.edu

Abstract

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 > or = 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/.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
19933825
[PubMed - indexed for MEDLINE]
PMCID:
PMC2804305
Free PMC Article
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