This rigorous process for evolutionary inference provides a means for accurate inference of GO annotations by homology, as well as a means for comparing and consistency-checking annotations for related genes. While earlier versions of PANTHER have allowed annotation of ‘subfamily nodes’ (i.e. ancestral genes that founded a particular subfamily), this more generalized GO annotation process requires all ancestral genes to be annotatable in principle, which has only become supported with the release of PANTHER 7. For most end users, perhaps the most relevant outcomes of this collaboration will be: (i) an increased number of GO annotations, especially those inferred by homology and (ii) the ability to trace all of the evidence behind each homology-based annotation. This evidence includes not only the gene that was experimentally demonstrated to perform a particular function (and the scientific publication reporting the experiment), but also the ancestral gene in which the function was inferred to have evolved. In the long term, all PANTHER ontology annotations will be migrated to this new standard.
