Local Function Conservation in Sequence and Structure Space
Figure 5
Comparing Similarity Scores to Raw and Combined Function Conservation Scores.
The ROC plot serves to analyze the reliability when inferring GO level three functional annotations from the nearest protein neighbors. For each protein domain, nearest neighbors are sought according to the four similarity measures (CE, TM, LP, GP). The GO terms attached to these nearest neighbors can be potentially inferred for a query protein. By sorting annotation transfers according to the similarity scores and evaluating the true positive rate versus the false positive rate, a ROC curve is derived.The black curve displays the average ROC curve for the four similarity measures (CE, TM, LP, GP); the boxplots attached serve to estimate the observed spread. Similarly, when sorting according to raw function conservation scores, we obtain four ROC curves, the average of which is shown as green curve along with the estimated spread as boxplots. Merging the information into a combined consensus score yields one score per inferred annotation; The corresponding ROC curve is plotted in violet for selective combination and in blue for consensus combination.