Table 1.
Interactome overconnectivity analysis of serum in ovarian cancer.
| Object name | Actual | n | R | N | Expected | Ratio | p-value | z-score |
|---|---|---|---|---|---|---|---|---|
| Transcription factors | ||||||||
| Nkx5-1 | 2 | 79 | 9 | 19603 | 0.036 | 55.14 | 5.668E-04 | 10.33 |
| NFIC | 4 | 79 | 104 | 19603 | 0.420 | 9.54 | 8.277E-04 | 5.56 |
| USF2 | 7 | 79 | 183 | 19603 | 0.738 | 9.49 | 9.061E-06 | 7.34 |
| Receptors | ||||||||
| ITGB6 | 2 | 79 | 9 | 19603 | 0.036 | 55.14 | 5.668E-04 | 10.33 |
| VLDLR | 3 | 79 | 22 | 19603 | 0.089 | 33.84 | 9.180E-05 | 9.8 |
| Glypican-1 | 2 | 79 | 16 | 19603 | 0.064 | 31.02 | 1.855E-03 | 7.64 |
| Ligands | ||||||||
| LAMA2 | 2 | 79 | 7 | 19603 | 0.028 | 70.9 | 3.324E-04 | 11.77 |
| CCL17 | 2 | 79 | 11 | 19603 | 0.044 | 45.12 | 8.614E-04 | 9.31 |
| Thrombospondin 2 | 2 | 79 | 15 | 19603 | 0.060 | 33.09 | 1.627E-03 | 7.91 |
| Kinases | ||||||||
| LRRK1 | 2 | 79 | 5 | 19603 | 0.020 | 99.26 | 1.591E-04 | 13.98 |
| Proteases | ||||||||
| CTRL | 1 | 79 | 1 | 19603 | 0.004 | 248.1 | 4.030E-03 | 15.72 |
| Mcpt8 | 1 | 79 | 1 | 19603 | 0.004 | 248.1 | 4.030E-03 | 15.72 |
| CRIM2 | 1 | 79 | 2 | 19603 | 0.008 | 124.1 | 8.044E-03 | 11.07 |
Actual = number of network objects in the activated dataset(s) which interact with the chosen object listed in object name column; n= number of network objects in the activated dataset( i.e. proteomics list); R=number of network objects in the complete database or background list which interact with the chosen object; N= total number of gene-based objects in the complete database or background list; Expected= mean of hypergeometric distribution (n·R/N); Ratio= connectivity ratio (Actual/Expected); z-score= (Actual-Expected)/s.d.(Expected), where s.d. - standard deviation of hypergeometric distribution, p-value= probability to have the given or higher (lower for negative z-score) value of Actual by chance under null hypothesis of no over- or under-connectivity.