- Article -
| In Silico Biology 4, 0026 (2004); ©2004, Bioinformation Systems e.V. |
GeneInfoViz: Constructing and visualizing gene relation networks
Mi Zhou and Yan Cui*
Department of Molecular Sciences, Center of Genomics and Bioinformatics, College of Medicine, University of Tennessee Health Science Center
Email: ycui2@utmem.edu
* corresponding author
Edited by E. Wingender; received January 27, 2003; revised and accepted March 27, 2004; published April 23, 2004
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.
Availability: http://genenet.org/
Key words: gene network, Gene Ontology, dynamic visualization