Table 1.

Enrichment P-values for overrepresented regulatory path motifs. Enrichment P-values for overrepresented regulatory path motifs in deletion and overexpression data with the two randomization methods described in the Methods. The complete tables for all 39 paths can be found in Tables S4 and S5 in Additional File 1).

Regulatory path	Perturbational data randomization	Physical network randomization
	Deletion data
TRI	7.3 × 10-38	4.08 × 10-34
TRI-TRI	6.95 × 10-7	1.41 × 10-4
TRI-PPI	5.66 × 10-3	1.77 × 10-2
PPI-TRI	1.96 × 10-17	1.87 × 10-10
PPI-PhI-TRI	8.10 × 10-3	1.4 × 10-3
PPI-TRI-TRI	2.01 × 10-3	2.1 × 10-3
	Overexpression data
TRI	1.1 × 10-13	2.46 × 10-9
TRI-TRI	2.74 × 10-7	2.02 × 10-2
PPI-TRI	1.21 × 10-7	7.54 × 10-4
PPI-PhI-TRI	2.59 × 10-5	8.20 × 10-4
PPI-TRI-TRI	1.58 × 10-7	3.27 × 10-4
TRI-PhI-TRI	6.17 × 10-8	6.32 × 10-2
TRI-PPI-TRI	1.96 × 10-4	6.12 × 10-2