Conceptualization of molecular findings by mining gene annotations

Contemporary genome-scale studies often return a long list of genes of potential interest, and a challenging task is to reveal the major functional themes the genes are involved in at a conceptual level. The Gene Ontology (GO) is an ontology representing molecular biology concepts related to genes and their products, and current annotations from the GO Consortium are highly specific. There is a need for tools that reveal the major functional themes through mining and representing semantic information of genes in an objective and quantitative manner. Our methods provide an objective and quantitative approach to capturing the major directions of gene functions in a context-specific fashion