Table 2.
Protein networks of statistical significance generated by Metacore (top four)
| No. | Elements | Processes | Size | Target | P-value ↑ | G-score |
|---|---|---|---|---|---|---|
| 1 | TCP1-beta, TCP1, tubulin alpha, c-myc, VHL, SP1, actin, tubulin gamma 1 etc. | actin filament depolymerization (5.7%; 3.375e − 07); actin filament polymerization (7.5%; 1.068e − 06); microtubule cytoskeleton organization and biogenesis (7.5%; 1.495e − 06); protein folding (13.2%; 1.570e − 06); regulation of progression through cell cycle (17.0%; 3.492e − 06) | 53 | 29 | 1.437e − 61 | 46.6395 |
| 2 | COX Va, cytochrome c oxidase, H2O2, c-myc, AP-1, caspase-3, calpastatin, tear lipocalin etc. | response to oxidative stress (8.2%; 7.512e − 05); induction of apoptosis (10.2%; 8.262e − 05); electron transport (12.2%; 9.994e − 05); vasodilation (4.1%; 2.522e − 04), glycolysis (6.1%; 2.816e − 04) | 51 | 28 | 1.897e − 59 | 46.5686 |
| 3 | HSP47, collagen V, SMAD3, c-myc, insulin, caspase-3, actin, alpha-2/beta-1 integrin etc. | phosphate transport (9.8%; 1.160e − 06); regulation of progression through cell cycle (15.7%; 2.251e − 05); induction of apoptosis by intracellular signals (5.9%; 4.448e − 05); actin filament polymerization (5.9%; 5.820e − 05); positive regulation of cell proliferation(11.8%; 5.839e − 05) | 51 | 28 | 1.897e − 59 | 48.3445 |
| 4 | GDI2, G3P2, RAB2A, huntingtin, OCT-1, SP1, c-myc, RAB-11A etc. | Notch signaling pathway (11.8%; 3.121e − 09); anagen (7.8%; 6.306e − 08); proteolysis during protein maturation (5.9%; 1.203e − 07); cell fate specification (7.8%; 3.371e − 07); chromosome organization and biogenesis (sensu Eukaryota) (9.8%; 5.548e − 07) | 51 | 26 | 6.094e − 54 | 46.5060 |
The table shows the elements (protein) in the network, the important processes involving these proteins, the number of nodes (size), the numbers of the seed target proteins included in the network and the statistical significance as P-value and G-score as defined in Materials and Methods. The networks were ranked based on the hypergeometric distribution representing the probability of a particular mapping of an experiment to a map (or network, or process etc.) to arise by chance, considering the number of proteins in the experiment versus the number of proteins in a map (resp. network, process, etc.) within the ‘full set’ of all proteins in all maps. P-values and G-scores are defined in Materials and Methods.