Table 2.
Summary of pairwise ‘candidate genes’ with their properties evaluated as ‘prevalent’ and ‘non-prevalent’ characters and their functional links having statuses with interaction scores vide SSS-I, SSS-II, SPPICS and WHMS values.
| S. no | Gene-pair | SSS-I Value (Property) |
SSS-II Value (Property) |
SPPICS Value (Property) |
WHMS Value |
|---|---|---|---|---|---|
| Prevalent | |||||
| 1 | FGFR1-PIK3CA | (0.54) Is_a | (0.81) Is_a | (0.97) Strong | 0.62 |
| 2 | ADAM10-ADAM17 | (0.56) Is_a | (0.77) Is_a | (0.86) Strong | 0.61 |
| 3 | AKT1-CTNNB1 | (0.49) Is_a | (0.79) Is_a | (0.99) Strong | 0.60 |
| 4 | AKT1-PIK3CA | (0.48) Is_a | (0.79) Is_a | (0.99) Strong | 0.59 |
| 5 | AKT1-ESR1 | (0.47) Is_a | (0.80) Is_a | (0.99) Strong | 0.59 |
| 6 | CTNNB1-ESR1 | (0.48) Is_a | (0.83) Is_a | (0.84) Strong | 0.58 |
| Non-prevalent | |||||
| 1 | AKT1-ATM | (0.54) Is_a | (0.71) Is_a | (0.80) Strong | 0.57 |
| 2 | CTNNB1-PSEN1 | (0.47) Is_a | (0.68) Part_of | (0.99) Strong | 0.56 |
| 3 | SQSTM1-VCP | (0.51) Is_a | (0.79) Is_a | (0.70) Weak | 0.56 |
| 4 | ADAM17-AKT1 | (0.50) Is_a | (0.78) Is_a | (0.74) Weak | 0.55 |
| 5 | AKT1-IL10 | (0.46) Is_a | (0.77) Is_a | (0.83) Strong | 0.55 |
| 6 | CHMP2B-SQSTM1 | (0.48) Is_a | (0.73) Is_a | (0.81) Strong | 0.55 |
| 7 | C9orf72-OPTN | (0.43) Is_a | (0.89) Is_a | (0.82) Strong | 0.55 |
| 8 | AKT1-MAPT | (0.45) Is_a | (0.73) Is_a | (0.80) Strong | 0.53 |
| 9 | CTNNB1-LRRK2 | (0.44) Is_a | (0.70) Part_of | (0.83) Strong | 0.53 |
| 10 | MAPT-PSEN1 | (0.45) Is_a | (0.64) Part_of | (0.89) Strong | 0.53 |
| 11 | AKT1-VCP | (0.42) Is_a | (0.80) Is_a | (0.78) Strong | 0.52 |
| 12 | ATM-ATRX | (0.44) Is_a | (0.79) Is_a | (0.71) Weak | 0.52 |
| 13 | C9orf72-ATXN2 | (0.40) Is_a | (0.86) Is_a | (0.75) Weak | 0.52 |
| 14 | CTNNB1-GLI2 | (0.45) Is_a | (0.85) Is_a | (0.61) Weak | 0.51 |
| 15 | AKT1-EIF4G1 | (0.48) Is_a | (0.67) Part_of | (0.65) Weak | 0.50 |
The prevalent pairwise ‘candidate genes’ are selected based on values of gene-pairs more than the cut-off value of WHMS viz. 0.57 (vide Fig. 5b and f). The terms ‘Is_a’ (subtype) and ‘Part_of’’ (component) represent the functional associations of GO-based terms hierarchically (ancestors-descendants relationship) organised in directed acyclic graph (DAG). The terms ‘Is_a’ and ‘Part_of’ properties are considered with the gene-pairs having scores greater than and less than, respectively the cut-off values of SSS-I (viz. 0.40) and SSS-II (viz. 0.71). The terms ‘Strong’ and ‘Weak’ represent the link strength having values of SPPICS to gene-pairs with scores greater than and less than, respectively the cut-off value (viz. 0.77). The cut-off values (optimal threshold score of ROC) are given in Fig. 5b.