Figure 2

Performance of different phylogenetic profile datasets and corrections. The predictive performance of the algorithm is illustrated by showing the fraction of known enzyme-encoding genes (x axis) predicted within different self-rank thresholds (y axis). For instance, dashed performance curve in subfigure a. (BLAST:xHG) shows that 30% of the test enzymes appear within the top 10 (out of 3352) candidates for their enzymatic function. a. Algorithm performance in predicting known E. coli metabolic enzymes based on the phylogenetic profile associations with the 1^st layer of the metabolic network neighborhood. Performance of a regular hypergeometric distribution is shown (HG), together with extended hypergeometric (xHG) and folding (xHG+folding) corrections. The scores are calculated on the BLAST-based dataset. b. The self-rank performance of the 1^st layer phylogenetic profile score, calculated using extended hypergeometric distribution with folding is shown for BLAST-based, KEGG-based and COG orthology datasets. The performance of the COG orthology dataset is corrected for the metabolic gene coverage bias.