GeneInfoViz: Constructing and Visualizing Gene Relation Networks

Article type: Research Article

Authors: Zhou, Mi | Cui, Yan

Affiliations: Department of Molecular Sciences, Center of Genomics and Bioinformatics, College of Medicine, University of Tennessee Health Science Center. E-mail: [email protected]

Note: [] Corresponding author

Abstract: Large amounts of knowledge about genes have been stored in public databases. One of the most challenging problems in Bioinformatics is, given all the information about the genes in the databases, determining the relationships between the genes. For example, how can we determine if genes are related and how closely they are related based on existing knowledge about their biological roles. We developed GeneInfoViz, a web tool for batch retrieval of gene information and construction and visualization of gene relation networks. We created a database containing compiled Gene Ontology information for the genes of several model organisms. Users can batch search for a group of genes and get the Gene Ontology terms that are associated with the genes. Directed acyclic graphs are generated to show the hierarchical structure of the Gene Ontology tree. GeneInfoViz calculates an adjacency matrix to determine whether the genes are related and, if so, how closely they are related based on biological processes, molecular functions, or cellular components they are associated with and then displays a dynamic graph layout of the network among the selected genes.

Keywords: gene network, gene ontology, dynamic visualization

Journal: In Silico Biology, vol. 4, no. 3, pp. 323-333, 2004