Genomics Inform.
2007 Sep;5(3):133-136.
GSnet: An Integrated Tool for Gene Set Analysis and Visualization
- Affiliations
-
- 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.
Keyword
- Full Text Links
-
- Actions
-
Cited
- CITED
-
- Close
- Share
-
- Similar articles
-
- TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data
- Interactive Visualization for Patient-to-Patient Comparison
- Discovery of Cellular RhoA Functions by the Integrated Application of Gene Set Enrichment Analysis
- A Visualization Tool for Computational Analysis of DNA Methylation Level Using Bisulfite Sequencing Data
- Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset
