Figure 3.

Enzyme predictions based on phylogenetic profiles. (a) The cumulative fraction of correctly predicted genes as a function of rank among all non-metabolic genes. All 6,093 non-metabolic yeast genes plus a known correct gene were ranked using Equation 2. The cumulative distribution is shown for ranks from 1 to 100; the inset shows the same distribution for all ranks. (b) The effect of connection specificity adjustment. Only highly ranked genes (1 to 50) are shown. (c) Comparison of the performance with all non-metabolic genes as candidates to that with only hypothetical genes as candidates for an orphan activity. (d) Predictions for the E. coli metabolic network. The cost function with the parameters optimized for the yeast network showed comparable performance to the cost function with the parameters specifically optimized for the E. coli network.