Gene Ontology term overlap as a measure of gene functional similarity

A New Method to Measure the Functional Similarity of Gene Products based on Gene Ontology

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 ...

simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes

MOTIVATION Measures of protein functional similarity are essential tools for function prediction, evaluation of protein-protein interactions (PPIs) and other applications. Several existing methods perform comparisons between proteins based on the semantic similarity of their GO terms; however, these measures are highly sensitive to modifications in the topological structure of GO, tend to be fo...

Methods of Normalization the Results of Gene Ontology Term Similarity

The article addresses the issue of improvement of the results quality when Gene Ontology (GO) term similarity is calculated. Several GO similarity measures produce results out of the range [0; 1]. Whereas, in order to compare different similarity measures or apply further processing, it is needed to normalise the results to this range. The most popular and well-known method of normalization is ...

Ontology-based Gene Set Enrichment Analysis Using an Efficient Semantic Similarity Measure and Functional Clustering

Gene set enrichment analysis allows to extract specific biological functions relative to a group of genes. To this aim, we propose here a novel approach for mining biological data, using the Gene Ontology (GO) as main source of genes annotation terms. Firstly, we will use our new semantic similarity measure (IntelliGO) in a clustering process, for grouping genes sharing similar biological funct...

Gene ontology for measuring similarity