Gene perturbation and intervention in context-sensitive stochastic Boolean networks

BMC Systems Biology

Table 1 Minimum sequence length and average run time in computing the state transition matrix (STM) for context-sensitive stochastic Boolean networks (CSSBNs)

n	k	Num	CSSBN (Norm 2 = 0.05)			CSSBN (Norm 2 = 0.03)			CSPBN[23]
			L(bits)	Average time(s)	Standard deviation	L(bits)	Average time(s)	Standard deviation	Average time(s)	Standard deviation
2	1	4	40	0.00148	0.00048	100	0.00181	0.00048	0.00049	0.00046
2	4	16	900	0.00553	0.00167	2000	0.01116	0.00036	0.01248	0.00251
2	16	64	1000	0.64383	0.41941	6000	1.02666	0.10779	0.09593	0.00901
3	1	8	140	0.00446	0.00132	340	0.00812	0.00094	0.00157	0.00045
4	1	16	250	0.01438	0.00287	750	0.03685	0.00268	0.00443	0.00027
4	16	256	8000	1.43115	0.01844	20000	3.29188	0.03830	1.66014	0.10349
5	1	32	420	0.04602	0.00261	1200	0.12341	0.00314	0.01862	0.00214
5	32	1024	8000	10.7359	0.01350	25000	35.5412	0.04335	24.0659	0.08390
6	1	64	600	0.09993	0.00458	1700	0.33797	0.00197	0.06662	0.00705
6	64	4096	24000	74.5058	1.20649	60000	195.793	4.86945	531.068	6.36186
7	1	32	1000	0.52519	0.02762	2800	1.34503	0.06377	0.25873	0.00719
7	16	2048	8000	18.8938	0.42939	25000	50.0857	0.27419	221.922	1.65582
8	1	256	1400	1.45711	0.02798	3500	3.67661	0.16084	1.05147	0.01302
8	4	1024	4000	5.50577	0.05167	12500	15.6728	0.11539	37.4102	2.20907
9	1	512	2600	5.36480	0.07636	8000	16.2693	0.14106	4.06749	0.06899
9	4	2048	8000	23.1989	0.40195	18000	45.9247	0.78522	72.4459	2.62472
10	1	1024	4000	18.4761	0.12540	11000	49.2457	0.36526	17.5134	0.12540
10	4	4096	10000	59.9416	0.41164	30000	162.686	1.13288	619.311	13.4098

n: the number of genes; k: the number of contexts. Perturbation and context switch probabilities: p = 0.1 and q = 0.8 (for k > 1). L: the required minimum sequence length for a given accuracy measured by Norm 2. Num: the number of states for the CSSBN. The results that at least one case of the CSSBN study is more efficient than the CSPBN, are highlighted in bold.

ISSN: 1752-0509