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The Gene Ontology (GO) provides biologists with a controlled terminology thatdescribes how genes are associated with functions and how functional terms arerelated to each other. These term-term relationships encode how scientistsconceive the organization of biological functions, and they take the form of adirected acyclic graph (DAG). Here, we propose that the network structure ofgene-term annotations made using GO can be employed to establish an alternatenatural way to group the functional terms which is different from thehierarchical structure established in the GO DAG. Instead of relying on anexternally defined organization for biological functions, our method connectsbiological functions together if they are performed by the same genes, asindicated in a compendium of gene annotation data from numerous differentexperiments. We show that grouping terms by this alternate scheme is distinctfrom term relationships defined in the ontological structure and provides a newframework with which to describe and predict the functions of experimentallyidentified sets of genes.

Finding New Order in Biological Functions from the Network Structure of Gene Annotations