Table II. The module partitions inferred from the established NP network and some control experiments.

Each control experiment was repeated 100 times, and P values were computed through a one-sample t test.

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

^aThe pseudomodule represents the module with few intramodule interactions.

^bThe control experiment was performed by shuffling expression profiles among genes.

^cThe control experiment was carried out by shuffling expression values of each gene among different time points.

^dThe control experiment was performed by shuffling PCC values among PPIs.

^eWe 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.