Anomaly-free Prediction of Gene Ontology Annotations Using Bayesian Networks

Gene and protein structural and functional annotations expressed through controlled terminologies and ontologies are paramount especially for the aim of inferring new biomedical knowledge through computational analyses. However, the available annotations are incomplete, in particular for recently studied genomes, and only a few of them are highly reliable human curated information. To support and speed up the time-consuming curation process, prioritized lists of computationally predicted annotations are hence extremely useful. In this paper we leverage a previous work on the automatic prediction of gene ontology annotations based on the singular value decomposition (SVD) of the gene-to-term annotation matrix, and we propose a novel post-processing method that uses a Bayesian network to eliminate predictions of anomalous annotations. In fact, we observed that the predicted annotation profiles might suggest that a gene shall be annotated to a term, but not to one of its ancestors, thus violating the constraint imposed by the gene ontology. To this end, the proposed algorithm processes the annotation profiles predicted by a SVD based method, and produces a ranked list of computationally discovered candidate annotations which is consistent with the gene ontology.