Table 1 Overview of the networks used in the evaluation process and the gold standards. Gold standard representation is shown in the original PPI network and in the selected networks. Edges signify the number of edges connecting GS Nodes in the network
From: ChainRank, a chain prioritisation method for contextualisation of biological networks
Application case | Network properties | Gold standard (GS) | Start protein | End protein | GS representation | ||
|---|---|---|---|---|---|---|---|
Edges | Nodes | Nodes | Edges | ||||
Human PPI network | 61872 | 10167 | IGF-Akt pathway | - | - | 13 | 20 |
COPD specific MAPK | - | - | 21 | 34 | |||
Muscle specific case | 847 | 308 | IGF-Akt pathway | IGF1 | RPS6KB1 | 9 | 10 |
COPD related case | 544 | 152 | COPD specific MAPK | EGFR | SRF, CREBBP, ELK1, MYC | 11 | 8 |