Comparison of positive predictive values in mediating domain pair prediction experiment. Estimated positive predictive value of the Association, EM, PE, and DPEA methods, and the performance expected by chance in such experiments, called the Random method. The results are presented according to the number of potential domain-domain interactions between the protein pairs in the set, and also in general. The numbers along the x-axis represent the number of protein pairs in the corresponding class. The PE method outperforms the previous methods in every class. In particular, for the 242 protein pairs with only 2 potential domain-domain interactions, PE has a PPV of 90.7%, and sensitivity of 93.8%, and for the 993 protein pairs with 2 to 6 potential domain-domain interactions, the PE method consistently has an average PPV above 76%. Overall, the PE method has an estimated average PPV of 75.3%. The Association and the EM methods both perform worse than Random; possible reasons for such an outcome are discussed in the text.
Guimarães et al. Genome Biology 2006 7:R104 doi:10.1186/gb-2006-7-11-r104