GoD: An R-Package based on Ontologies for Prioritization of Genes with respect to Diseases

Omics sciences are widely used to analyze diseases at a molecular level. Usually, results of omics experiments are a large list of candidate genes, proteins or other molecules. The interpretation of results and the filtering of candidate genes or proteins selected in an ex- periment is a challenge in some scenarios. This problem is particularly evident in clinical scenarios in which researchers are interested in the behaviour of few molecules related to some specific disease. The filtering requires the use of domain-specific knowledge that is often encoded into ontologies. To support this interpretation, we implemented GoD (Gene ranking based On Diseases), an algorithm that ranks a given set of genes based on ontol- ogy annotations. The algorithm orders genes by the semantic similarity computed between annotation of each gene and those describing the selected disease. We tested as proof-of- principle our software using Human Phenotype Ontology (HPO), Gene Ontology (GO) and Disease Ontology (DO) using the semantic similarity measures. The dedicated website is https://sites.google.com/site/geneontologyprioritization/.