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GSnet: An Integrated Tool for Gene Set Analysis and Visualization  

Choi, Yoon-Jeong (Nano Materials Simulation and Fabrication Laboratory, Department of Materials Science and Engineering, KAIST)
Woo, Hyun-Goo (aboratory of Experimental Carcinogenesis, National Cancer Institute, NIH)
Yu, Ung-Sik (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)
Publication Information
Genomics & Informatics / v.5, no.3, 2007 , pp. 133-136 More about this Journal
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.
Keywords
microarray analysis; gene set analysis; protein-protein interaction network; network visualization;
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