The GO Term Matrix (18) can be used to query and visualize GO term co-annotation patterns. It has been used as part of a GO annotation quality control system to identify annotation errors and build annotation rules. These rules state that certain annotations cannot co-occur, for example few or no proteins play roles in both DNA replication and cytoskeleton organization. One annotation, to Pdgfb (platelet derived growth factor subunit B), a hormone, was identified as annotated to both terms. After review of the original paper, it was noticed that the DNA replication annotation was incorrect: DNA synthesis was used as a readout for a growth/proliferation phenotype, but as expected, Pdgfb does not itself play a role in DNA replication.
