A common language to describe genes from flies, yeast, and mice. K. Dolinski ¹, C.A. Ball ¹, S.S. Dwight ¹, M.A. Harris ¹, L. Issel-Tarver ¹, A. Kasarskis ¹, S. Lewis ², M. Ringwald ³, J.T. Eppig ³, J.E. Richardson ³, J.A. Blake ³, M. Ashburner ⁴, D. Botstein ¹, J.M. Cherry ¹. 1) Genetics Department, Stanford University, Stanford, CA, USA; 2) Drosophila Genome Project/FlyBase, Berkeley, CA, USA; 3) Mouse Genome Informatics, Jackson Labs, Bar Harbor, ME, USA; 4) FlyBase/EBI, Cambridge, UK.

   The number of complete genome sequences is increasing rapidly. To meet the growing need for consistent annotation of genes and their products in different organisms, the Saccharomyces Genome Database (SGD) is collaborating with FlyBase, the Mouse Genome Database (MGD), and Gene Expression Database (GXD). This joint effort, the Gene Ontology (GO) project, is creating a set of three independently organized controlled vocabularies, or gene ontologies. Process describes broad biological goals, such as mitosis. Function describes the tasks performed by individual gene products; examples are transcription factor and DNA binding. Cellular component encompasses subcellular complexes and locations, such as nucleus and telomere. Within each ontology, parent-child relationships between terms are defined, and a gene may be annotated to any level in an ontology. Curators from each database are mapping genes to terms from the three GO categories. Because there are experimental data for more than 50% of yeast genes, GO annotation of yeast genes provides a powerful tool for learning more about corresponding genes in other species. GO annotation is also useful in the interpretation of microarray experiments in which the expression of thousands of genes is assayed simultaneously, and genes with similar expression patterns are grouped into clusters. GO annotation of clustered genes reveals that genes involved in a process often show similar expression patterns, while functions correlate with expression less often. Further, the combination of microarray clustering and biological process annotation may suggest roles for uncharacterized genes. URL: www.geneontology.org.