GoD: An R-package based on ontologies for prioritization of genes with respect to diseases

Abstract

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 experiment 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 ontology annotations. The algorithm orders genes by the semantic similarity computed with respect to a disease among the annotations of each gene and those describing the selected disease. We tested GoD as proof-of-principle using: Human Phenotype Ontology (HPO), Gene Ontology (GO) and Disease Ontology (DO) using the semantic similarity measures. GoD is publicly available for academic use at https://sites.google.com/site/geneontologyprioritization/.