Table 8 |
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|
Comparison of the predicted SSL network to the known SSL network |
|||||||
|
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 |
|
|
|
|||||||
|
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. |
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|
Paladugu et al. BMC Bioinformatics 2008 9:426 doi:10.1186/1471-2105-9-426 |
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