Table II. The module partitions inferred from the established NP network and some control experiments.
Treatment | Protein/Module |
Intramodule PPI/Module |
No. of Modules |
Overlap with the Established NP Network | No. of Pseudomodulesa | |||
Average | P | Average | P | Average | P | |||
The established NP network | 193.3 | – | 65.4 | – | 7 | – | – | 0/1 |
Shuffle among genesb | 142.0 | 3.45 × 10−37 | 34.9 | 4.43 × 10−47 | 9.1 | 1.07 × 10−23 | 68.9% | 18/100 |
Shuffle expression valuesc | 71.6 | 3.80 × 10−102 | 8.6 | 5.50 × 10−135 | 14.4 | 6.91 × 10−41 | 56.5% | 45/100 |
Shuffle PCCsd | 15.6 | 8.60 × 10−200 | 0.4 | 8.10 × 10−281 | 90.4 | 2.03 × 10−89 | 74.9% | 100/100 |
Randomized networke | 178.1 | 8.23 × 10−5 | 53.1 | 1.58 × 10−9 | 7.7 | 1.50 × 10−5 | 63.6% | 19/100 |
The pseudomodule represents the module with few intramodule interactions.
The control experiment was performed by shuffling expression profiles among genes.
The control experiment was carried out by shuffling expression values of each gene among different time points.
The control experiment was performed by shuffling PCC values among PPIs.
We randomized the NP network while keeping the degree distribution, which was used to test whether an artificial network that has the same topology as the established NP network can result in the same module partition.