Table 2:

K-partite simulation study to evaluate k optimally: in each cell we summarize the mean number (across 100 simulations) of falsely grouped edges and its standard deviation. Each row shows the results based on a δ that is the difference of differentially and non-differentially expressed edges and in each column. In each column, we set K equal to 2, 4, or 10. The choice of K is robust to noise and the number of independent sets.

Difference δ	K = 2		K = 4		K = 10
	FP	FN	FP	FN	FP	FN
2.50	0.08±0.94	0.75±1.59	0.29±1.52	0.92±1.20	1.21±1.85	1.50±1.24
3.00	0.02±0.14	0.78±1.52	0.47±2.01	0.82±1.16	1.03±1.82	1.36±1.10
3.50	0.08±1.05	0.81±1.69	0.42±1.89	0.94±1.25	0.96±1.70	1.36±1.11
4.00	0.06±0.71	0.58±1.32	0.22±1.41	0.88±1.11	1.07±1.87	1.32±1.21
4.50	0.09±0.10	0.84±1.66	0.41±1.85	0.77±1.11	1.10±1.89	1.46±1.21
5.00	0.16±1.50	0.91±1.68	0.45±1.91	0.86±1.20	0.89±1.84	1.46±1.13