PrOnto database : GO term functional dissimilarity inferred from biological data

Abstract

Moonlighting proteins are defined by their involvement in multiple, unrelated functions. The computational prediction of such proteins requires a formal method of assessing the similarity of cellular processes, for example, by identifying dissimilar Gene Ontology terms. While many measures of Gene Ontology term similarity exist, most depend on abstract mathematical analyses of the structure of the GO tree and do not necessarily represent the underlying biology. Here, we propose two metrics of GO term functional dissimilarity derived from biological information, one based on the protein annotations and the other on the interactions between proteins. They have been collected in the PrOnto database, a novel tool which can be of particular use for the identification of moonlighting proteins. The database can be queried via an web-based interface which is freely available at http://tagc.univ-mrs.fr/pronto.

Keywords: database; functional similarity; gene ontology; moonlighting protein; protein-protein interactions.

Figure 1

PrOnto probabilities principle. The blue set represents the proteins annotated to GO1, the red set represents proteins annotated to GO2. The intersection corresponds to either proteins annotated to both terms (APs) or interactions involving proteins annotated to both terms (IPs).

Figure 2

PrOnto web interface. In the example shown, two terms have been submitted. The lower panel shows the results for APs.