Genomics & Informatics  2007;5(3):133-136

GSnet: An Integrated Tool for Gene Set Analysis and Visualization.

Yoon Jeong CHOI 1 ; Hyun Goo WOO ; Ungsik YU

Affiliations

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Keywords

microarray analysis; gene set analysis; proteinprotein interaction network; network visualization

Country

Republic of Korea

Language

English

Abstract

The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.