GOtoGene: A Method for Determining the Functional Similarity among Gene Products

We present in this paper novel techniques that determine the semantic relationships among genes and gene products. We implemented these techniques in a middleware system called GOtoGene, which resides between user application and Gene Ontology database. Given a set S of genes, GOtoGene would return another set S  of genes, where each gene in S  is semantically related to each gene in S . The framework of GOtoGene refines the concept of Lowest Common Ancestor by defining the concept of Semantically Relevant Lowest Common Ancestor using the concept of existence dependency. We evaluated GOtoGene experimentally and compared it with three other methods. Results showed marked improvement.