Summary of biological pathway prediction accuracies of physical and functional protein-protein interaction prediction methods.

The performance summary of protein-protein prediction methods measured as Area Under the ROC Curve (AUC). Pathway prediction accuracies of various methods differ significantly with Wilcox test p-value <3.582e–13. These methods include Gene Neighbor, Gene Cluster, Expression Similarity, Phylogenetic Profiling and Genome distance-Mirrortree abbreviated as GN, GC, ES, PP and GM respectively. E. coli pathways are based on the 2nd level KEGG orthology definition with 50 or more protein components only.