A new gene ontology-based measure for the functional similarity of gene products.

BACKGROUND: Although biomedical ontologies have standardized the representation of gene products across species and databases, a method for determining the functional similarities of gene products has not yet been developed. METHODS: We proposed a new semantic similarity measure based on Gene Ontology that considers the semantic influences from all of the ancestor terms in a graph. Our measure was compared with Resnik's measure in two applications, which were based on the association of the measure used with the gene co-expression and the protein-protein interactions. RESULTS: The results showed a considerable association between the semantic similarity and the expression correlation and between the semantic similarity and the protein-protein interactions, and our measure performed the best overall. CONCLUSION: These results revealed the potential value of our newly proposed semantic similarity measure in studying the functional relevance of gene products.