GO(vis), a gene ontology visualization tool based on multi-dimensional values.
Most of gene product similarity measurements concentrate on the information content of Gene Ontology (GO) terms or use a path-based similarity between GO terms, which may ignore other important information contained in the structure of the ontology. In our study, we integrate different GO similarity measure approaches to analyze the functional relationship of genes and gene products with a new triangle-based visualization tool called GO(Vis). The purpose of this tool is to demonstrate the effect of three important information factors when measuring the similarity between gene products. One advantage of this tool is that its important ratio can be adjusted to meet different measuring requirements according to the biological knowledge of each factor. The experimental results demonstrate that GO(Vis) can display diagrams of the functional relationship for gene products effectively.
Ning
Zi
Z
Department of Computer Science and Technology, East China Normal University, Shanghai 200241, China.
Jiang
Zhenran
Z
D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D012660:Semantics; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D009626:Terminology as Topic; D014584:User-Computer Interface