Evaluation of Semantic Term and Gene Similarity Measures

Abstract

In this paper we present the results of the research verifying how the functional description of genes contained in Gene Ontology database is related to genes expression values recorded during biological experiments. We compare several different gene similarity measures and semantic term similarity measures, and evaluate how the similarity of genes based on Gene Ontology terms is correlated with similarity of genes based on expression profiles. The analysis are preformed on three different datasets and we show that there is no single term similarity measure that always gives the best correlation results. The choice of the best term similarity measure depends on dataset characteristic.