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Table 8 Comparison of the predicted SSL network to the known SSL network

From: Mining protein networks for synthetic genetic interactions

Threshold Level (Number of pre dictions) Gene-pair Characteristic S∩C Sonly Conly S'∩C' Odds P-value
Known SSL Pairs (6074) Cellular Component 4467 1607 193007 207466 2.988 < 2.2 × 10-16
  Molecular Function 1464 4610 38865 361608 2.955 < 2.2 × 10-16
  Biological Process 4074 2000 137827 262646 3.882 < 2.2 × 10-16
  Protein Complex 197 5877 747 399726 17.937 < 2.2 × 10-16
  Upstream Regulator 220 5854 10327 390146 1.420 9 × 10-7
0.75 (30087) Cellular Component 17967 12120 781640 799150 1.516 < 2.2 × 10-16
  Molecular Function 4115 25972 113100 1467690 2.056 < 2.2 × 10-16
  Biological Process 12966 17121 314562 1266228 3.048 < 2.2 × 10-16
  Protein Complex 363 29724 1339 1579451 14.405 < 2.2 × 10-16
  Upstream Regulator 1052 29035 47294 1533496 1.175 3.76 × 10-7
0.80 (28440) Component 16942 11498 782665 799772 1.506 < 2.2 × 10-16
  Function 3826 24614 113389 1469048 2.014 < 2.2 × 10-16
  Process 12245 16195 315283 1267154 3.039 < 2.2 × 10-16
  Protein Complex 346 28094 1356 1581081 14.360 < 2.2 × 10-16
  Upstream Regulator 986 27454 47360 1535077 1.164 3.01 × 10-6
0.850 (5149) Component 3799 1350 795808 809920 2.864 < 2.2 × 10-16
  Function 1309 3840 115906 1489822 4.382 < 2.2 × 10-16
  Process 3221 1928 324307 1281421 6.601 < 2.2 × 10-16
  Protein Complex 287 4862 1415 1604313 66.927 < 2.2 × 10-16
  Upstream Regulator 173 4976 48173 1557555 1.124 0.024
0.900 (1398) Component 1184 214 798423 811056 5.602 < 2.2 × 10-16
  Function 508 890 116707 1492772 7.301 < 2.2 × 10-16
  Process 1060 338 326468 1283011 12.325 < 2.2 × 10-16
  Protein Complex 151 1247 1551 1607928 125.535 < 2.2 × 10-16
  Upstream Regulator 49 1349 48297 1561182 1.174 0.1525
0.950 (953) Component 831 122 798776 811148 6.917 < 2.2 × 10-16
  Function 368 585 116847 1493077 8.038 < 2.2 × 10-16
  Process 776 177 326752 1283172 17.217 < 2.2 × 10-16
  Protein Complex 126 827 1576 1608348 155.485 < 2.2 × 10-16
  Upstream Regulator 29 924 48317 1561607 1.014 0.4958
0.999 (202) Component 184 18 799423 811252 10.373 < 2.2 × 10-16
  Function 93 109 117122 1493553 10.880 < 2.2 × 10-16
  Process 179 23 327349 1283326 30.511 < 2.2 × 10-16
  Protein Complex 37 165 1665 1609010 216.702 < 2.2 × 10-16
  Upstream Regulator 5 197 48341 1562334 0.820 0.7274
  1. Association between SSL interaction and gene-pair characteristic, following the framework of [20]. S ∩ C represents the number of gene pairs with both SSL interaction(S) and same gene-pair characteristic(C). Sonly represents the number of gene pairs with SSL interaction only. Conly represents the number of non-SSL gene pairs that share the same characteristic. S' ∩ C' represents the number of gene pairs that neither have SSL interaction nor share a specified characteristic. Odds represents the odds ratio of a SSL pair sharing a given characteristic to a non-SSL pair sharing the same characteristic. The P-value represents the statistical significance of overlap between SSL interaction and the specified characteristic as computed by Fisher's exact test. If a protein corresponding to a gene is not assigned to any of the known protein complexes then the gene and its interacting partner are considered to come from two different protein complexes. Similarly in the case of upstream regulators, if a gene does not have any known upstream regulator then the gene and its interacting partner are treated as if they don't share any common upstream regulator. The P-values are not significant in case of common upstream regulator due to the fact the number of predicted positives that share a common upstream regulator is very small in comparison to the total number of pairs that share a common upstream regulator, which is also reflected in the low odds ratio seen at different levels of threshold.