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Genomics Inform > Volume 5(3); 2007 > Article
GSnet: An Integrated Tool for Gene Set Analysis and Visualization.
Yoon Jeong Choi, Hyun Goo Woo, Ungsik Yu
1Nano Materials Simulation and Fabrication Laboratory, Department of Materials Science and Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
2Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, USA.
3Korean BioInformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea. ungsik@kribb.re.kr
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; proteinprotein interaction network; network visualization


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