Using gene ontology on genome-scale studies to find significant associations of biologically relevant terms to groups of genes

The analysis of genome-scale data from different high throughput techniques usually involves the grouping of genes based on experimental criteria. These groups are a consequence of the biological roles the genes are playing within the cell. Establishing which of these groups are functionally important is essential. Gene ontology terms provide a specialised vocabulary to describe the relevant biological properties of genes. We used a simple procedure to extract terms that are significantly over or under-represented in sets of genes within the context of a genome-scale experiment. Said procedure, which takes the multiple-testing nature of the statistical contrast into account, has been implemented as a Web application, FatiGO, allowing for easy and interactive querying. Several examples demonstrate its application and the type of information that can be extracted. Although a number of genes still lack gene ontology annotations, the results were informative enough to characterise the biological processes in the systems analysed.