Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components
Figure 2
Performance evaluation of inferred networks.
We predicted 30 S. cerevisiae interaction networks, each representing one interaction type. A) To evaluate the overall accuracy of these networks, we withheld ∼30% of the genes in our gold standard as a test set. Performance on this test set averaged an AUC of 0.79 across all interaction types in the ontology; see Text S1 for individual ROCs. B) To specifically assess the accuracy with which interaction directionality was predicted (as opposed to the presence/absence of interactions in part A), we tested the frequency with which an interaction's correct direction was ranked above its incorrect direction in each of the 12 directed interaction networks. These results are uniformly well above random (0.5), supporting our ability to accurately predict both the presence and the directionality of many specific types of protein interactions.