Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: three tool comparison

In genomic and molecular biology domains, controlled vocabularies and ontologies are becoming of paramount importance to integrate and correlate the massive amount of information increasingly accumulating in heterogeneous and distributed databanks. Although at present they are still few and present some issues, they can effectively be used also to biologically annotate genes on a genomic scale and across different species, and to evaluate the relevance of such annotations. Here, we compare three tools using the Gene Ontology and genomic controlled vocabularies to statistically highlight significant biological characteristics of gene sets to help in the biological interpretation of high-throughput experiment results and knowledge discovery from data.