Figure 4

Importance of metabolic neighborhood for the predictive power of the algorithm. (a) Informative and non-informative gaps. About one-third of the gaps did not allow any discrimination between the correct and average genes (represented by bin 0 in the figure), that is, the function value of the correct gene is equal to or smaller than the function value for average genes determined by Equation 2. The red line shows the average rank of correct genes represented in each bin. Genes filling gaps with higher discrimination ratios are ranked higher by the algorithm. (b) The relationship between the rank of a correct enzyme in a gap and the average correlation of first layer genes around the gap. A metabolic gene for a gap with a high average first layer correlation (>0.5) is usually highly ranked by the prediction algorithm (black line) but the fraction of such gaps is small (red bins).