BMC Systems Biology

Table 6 Sample experiment output with constitutively active Ras.

From: ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

		Average Inputs									Average Outputs
Global Output	Count	ECM	EGF	ExtPump	alpha_q Ligand	alpha_i Ligand	alpha_s Ligand	alpha_12_13 Ligand	IL1_TNF	Stress	Akt	Erk	Cdc42	Rac
2200	229	39	62	37	51	50	49	51	2	2	49	79	4	3
2211	172	83	46	42	46	48	45	52	2	2	42	75	18	15
2210	153	55	69	53	51	52	51	49	2	2	48	82	15	5
1000	142	19	23	64	51	46	47	45	2	2	19	3	1	1
2000	75	11	62	44	54	54	50	56	1	2	42	3	0	0
1211	45	87	24	71	48	46	53	54	2	2	23	63	16	19
2100	32	13	78	61	49	51	48	51	3	2	49	15	1	0
2201	28	83	46	22	46	56	51	57	2	2	46	76	6	14
1200	25	41	27	77	48	50	43	47	2	2	22	61	5	4
1201	21	75	9	65	57	48	46	47	2	2	21	58	5	17
1210	16	54	37	83	48	61	38	50	2	2	23	64	14	6
2221	13	89	68	57	43	35	53	49	2	1	46	79	32	15
1001	6	58	11	49	43	26	52	53	1	3	16	1	5	11
2220	5	79	92	86	39	82	33	45	3	2	57	88	32	8
1100	5	32	12	46	45	65	44	57	2	2	22	18	6	4
1011	4	66	13	71	24	33	60	45	2	2	14	2	19	14
1010	4	50	14	88	63	66	46	62	1	2	15	1	16	7
2110	3	36	35	29	31	64	55	55	3	1	34	18	11	5
1212	2	95	4	50	40	65	68	91	2	1	23	56	12	31
1110	2	60	39	84	71	61	26	81	5	3	23	19	19	8
0011	2	67	1	91	54	5	46	74	2	4	8	2	10	17
1202	2	90	5	61	68	53	41	51	2	4	19	57	9	30
1111	2	67	16	100	55	89	80	20	2	3	13	16	24	15
0001	1	71	0	64	68	4	97	69	5	1	8	5	6	17
0100	1	47	16	100	31	13	1	85	3	5	9	15	4	6
0201	1	92	3	100	73	92	85	82	2	5	5	53	6	29
2212	1	99	15	47	59	24	32	17	4	0	34	64	23	30
0010	1	29	20	98	73	7	71	63	1	5	7	1	11	3
1002	1	98	3	58	43	5	59	70	5	3	13	5	9	33
1221	1	100	38	87	95	40	79	51	0	1	23	69	33	26
1021	1	81	23	88	73	10	78	22	1	0	15	1	34	21
0212	1	100	9	99	62	54	19	3	5	1	9	57	17	34
2111	1	50	14	24	41	90	22	32	3	0	31	27	18	10
0202	1	100	4	90	41	49	39	48	5	5	9	55	2	33
0211	1	75	9	96	80	91	95	21	1	3	8	57	11	17

Similarly to Table 5, results summarized in this table were generated during an experiment consisting of 1,000 simulation with the same paremeters (e.g., all dosages were selected randomly in a stress limited environment, discretization, etc.). Contrary to the simulation from Table 5 however, in this example, cells were simulated with constitutively active Ras. Results of this experiment show a marked increase in Erk activity (as has been suggested by laboratory research, [24, 25]), simulating a growth-factor independent activation of Erk. This phenomena can be easily seen either in the Global Output and Count columns where 229 of the 1,000 simulations produced the '2200' pattern (global output) and over 500 simulations resulted in '22XX' or the Average Output column which shows that the majority of external-input combinations resulted in Erk average activity of 75–82%.

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