Figure 5
Histograms of probabilities assigned to experimentally observed interactions in yeast (a), worm (b), and fly (c).
Figure 6
Modular structure of conserved protein clusters among yeast and worm. The overview graph represents 220 conserved protein clusters (cluster ID numbers are given within each square). Each link indicates an overlap between clusters, where thickness is proportional to the percentage of shared proteins (intersection/union). Colors highlight clusters that are significantly enriched for proteins involved in the same GO cellular process (p < 0.05, corrected for multiple testing). Clusters grouped into a single square share >15% overlap with at least one other cluster in the group, and are all of the same significant cellular process.Figure 7
Modular structure of conserved protein clusters among yeast and fly. The overview graph represents 835 conserved protein clusters. See legend of Suppl. Figure 2 for details.Figure 8
Modular structure of conserved proteins clusters among worm and fly. The overview graph represents 132 conserved protein clusters. See legend of Suppl. Figure 2 for details.Figure 9
Conserved clusters detected in pairwise but not three-way network alignments. Representative clusters are shown from the yeast/fly [a-e], yeast/worm [f-h] and worm/fly [i-l] pairwise comparisons; these clusters were distinct (< 10% overlap) from those detected in the three-way alignment. Proteins from yeast (orange ovals), worm (green rectangles) or fly (blue hexagons) are connected by direct (thick link) or indirect (distance 2; thin link) protein-protein interactions. Horizontal dotted gray links indicate cross-species sequence similarity.Figure 10
Conserved paths among yeast, worm and fly. See legend of Suppl. Figure 5 for details.Figure 11
Comparison of 2-way and 3-way clusters. Shown are Venn diagrams depicting the relationships between the computed 2-way and 3-way clusters in terms of the number of distinct proteins that are included in each set of clusters.
Table 3
Species #Correct #Predictions Success rate Yeast-Worm 93 216 43% Yeast-Worm 54 121 45% Yeast-Fly 280 637 44% Yeast-Fly 208 517 40% Worm-Fly 22 55 40% Worm-Fly 34 67 51% Yeast-Worm-Fly 114 198 58% Yeast-Worm-Fly 57 95 60% Yeast-Worm-Fly 115 184 63% Cross-validation results for predicting protein GO Biological Processes. Entries are: the alignment graph used for predicting functions for the species that appears in bold-type; the number of correct predictions; the total number of predictions; and the success rate.
Table 4
Species #Correct #Predictions Success rate Yeast-Worm 61 179 34% Yeast-Worm 40 118 33% Yeast-Fly 171 488 35% Yeast-Fly 156 402 39% Worm-Fly 37 64 58% Worm-Fly 31 61 51% Yeast-Worm-Fly 79 162 49% Yeast-Worm-Fly 51 103 49.5% Yeast-Worm-Fly 77 149 52% Cross-validation results for predicting protein GO Biological Processes. Entries are: the alignment graph used for predicting functions for the species that appears in bold-type; the number of correct predictions; the total number of predictions; and the success rate.
Table 5
Species TP FN TN FP Sensitivity Specificity p-value Yeast-Worm 51 149 287 18 26% 94% 1.3e-13 Yeast-Worm 42 48 29 5 47% 85% 1.3e-13 Yeast-Fly 77 311 624 42 20% 94% 1.3e-14 Yeast-Fly 67 88 101 28 43% 78% 3.9e-14 Worm-Fly 37 161 133 16 19% 89% 3e-4 Worm-Fly 49 141 126 15 26% 89% 1.4e-8 Yeast-Worm-Fly 117 117 262 80 50% 77% 1.1e-25 Yeast-Worm-Fly 54 72 53 12 43% 82% 1e-13 Yeast-Worm-Fly 54 182 178 33 23% 84% 5.3e-5 (*)Yeast-Worm-Fly 20 214 339 3 9% 99% 1.2e-6 (*)Yeast-Worm-Fly 13 113 65 0 10% 100% 6e-4 (*)Yeast-Worm-Fly 1 235 211 0 0.4% 100% 0.5 Cross-validation results for protein interaction predictions. Entries are: the alignment graph used for predicting interactions for the species that appears in bold-type; overall numbers of true positives (TP), false negatives (FN), true negatives (TN), and false positive (FP) predictions; specificity and sensitivity of the predictions; and a hypergeometric p-value of the results. An asterisk denotes that the predictions were made by further requiring the two proteins to be included in a conserved path or cluster.
Table 6
Species #Proteins #Proteins in sub-networks Coverage Yeast-Worm 765 271 35% Yeast-Worm 536 204 38% Yeast-Fly 1,494 790 53% Yeast-Fly 1,559 778 50% Worm-Fly 852 246 29% Worm-Fly 1,131 291 26% Yeast-Worm-Fly 801 219 27% Yeast-Worm-Fly 551 190 34% Yeast-Worm-Fly 911 240 26% Protein coverage by clusters and paths. For each alignment graph and each species (appearing in bold-type), given are the number of distinct proteins for this species in the corresponding alignment graph, the number of proteins that are covered by significant clusters and paths, and the percent of coverage.