Gene Ontology term overlap as a measure of gene functional similarity

Background: The availability of various high-throughput experimental and computational methods allows biologists to rapidly infer functional relationships between genes. It is often necessary to evaluate these predictions computationally, a task that requires a reference database for functional relatedness. One such reference is the Gene Ontology (GO). A number of groups have suggested that the semantic similarity of the GO annotations of genes can serve as a proxy for functional relatedness. Here we evaluate a simple measure of semantic similarity, term overlap (TO). Results: We computed the TO for randomly selected gene pairs from the mouse genome. For comparison, we implemented six previously reported semantic similarity measures that share the feature of using computation of probabilities of terms to infer information content, in addition to three vector based approaches and a normalized version of the TO measure. We find that the overlap measure is highly correlated with the othe...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Meeta Mistry, Paul Pavlidis
• Keywords: BMCBI 2008, Computational Methods, Functional Relatedness, Semantic Similarity