Fig. 12

A hypothetical representation showing how the network integration filters false positive interactions. This scenario compares candidate gene predictions between a a PPI network and an b anatomy-based gene network. The nodes A, B, and C (colored in black) in both networks represent three genes known to be associated with a certain anatomical entity denoted as entity 1. In the PPI network (a), genes D and F are predicted to be associated with entity 1 because genes D and F interact with genes A, B, and C that are known to be associated with the entity 1. In contrast, the anatomy-based gene network (b) only predicts D as a potential candidate for entity 1 because the gene F does not have any interaction with other genes annotated with entity 1. The absence of interactions of gene F in gene network (b) can be due to two reasons: (1) it is not annotated with any anatomical entities, (2) it is not annotated with entities that are similar to the anatomy entities associated with genes A, B, or C. The anatomy-based gene network (b) is built entirely on anatomy ontology information, thus it provides a different interaction structure. Hypothetically, the gene F could have formed false positive interactions in the PPI network, and the integrative use of the anatomy-based gene network may reduce the false positives by filtering them