Gene ontology application to genomic functional annotation, statistical analysis and knowledge mining.

Abstract

While a massive amount of biomolecular information is increasingly accumulating in different databanks, on the other hand high-throughput technologies are generating a great quantity of data that need to be annotated with the genomic information available, and interpreted. To this aim, the use of specific ontologies can greatly help either in integrating different information stored within heterogeneous databanks, or in identifying and clustering sequence data sharing common characteristics. In the molecular biology domain, the Gene Ontology (GO) is the most developed and widely used ontology. To demonstrate its great utility in the annotation and biological interpretation of gene sets obtained by means of high-throughput experiments, we implemented the web application here described. It enables functional annotations of a given gene set on a genomic scale and across different species. Within our application the annotations provided by the GO vocabulary allow either to easily bind several information from different resources, or to cluster annotated genes according to their biological characteristics. Through the GO structure it is also possible to represent biological concepts with different specificity levels, from very general to very precise concepts. Furthermore, the statistical evaluation of the categorizations provided by the GO annotations enables to highlight the most significant biological characteristics of a gene set, and therefore to mine knowledge from data. Our created tool meets the need to manage a vast quantity of biological data with a simple user interface adapt also for users with limited informatics knowledge, leading them to evaluate the functional significance of experiment's results with graphical views and statistical indexes in a well-known web browser user interface.