Figure 3.

The performance of the co-citation algorithm at identifying protein interactions. (a) The probabilistic score effectively ranks co-cited proteins by their tendency to participate in the same pathway, as measured on the functional annotation training benchmark. As the probability of random co-citation decreases, the functional relatedness of the co-cited proteins increases. This tendency is robust to changes in the CRF confidence threshold chosen (data not shown). Each point represents 3,000 protein pairs. (b) An examination of the number of protein pairs identified at different CRF thresholds (0.8, 0.6, and 0.4) shows that the recall of the method is increased with lowered thresholds. Re-ranking the 15,000 top-scoring protein pairs (CRF threshold = 0.8) by the tendency of the abstracts to discuss physical protein interactions shows their consistent performance in the annotation benchmark.