Table 2.

The percentages of generated networks with scores better than one of the original network. In the options of the algorithm with forbidden or forced self-loops, the original network was modified by removing or adding appropriate edges, respectively.

dataset		all regulatory interactions			transcriptional regulation only
perturbations	time points	s-l forb.	s-l perm.	s-l forc.	s-l forb.	s-l perm.	s-l forc.
-	12	12.642	24.309	53.245	02.925	02.876	20.842
knockout	12	00.000	00.009	03.901	00.015	00.119	05.328
knockout	3	00.000	00.001	08.661	00.001	00.000	04.330
both	3	00.000	00.003	09.642	00.000	00.005	04.618