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Table 5 Sample output generated by the Patterns extension.

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
1000 218 23 26 55 51 50 45 55 2 2 20 3 1 1
2000 157 23 67 38 45 47 51 50 1 2 43 4 2 1
2100 96 29 78 40 50 44 44 54 4 2 48 14 3 2
2110 96 60 76 48 48 55 53 48 2 2 47 15 17 6
1011 77 73 21 55 46 60 50 53 2 2 20 5 18 15
2111 62 85 68 34 54 53 49 58 2 2 43 16 21 13
2010 46 54 65 54 47 50 52 45 1 2 40 5 15 5
1010 41 49 30 66 43 48 52 46 2 2 20 4 15 6
2121 37 88 70 54 54 58 48 41 2 1 41 17 38 14
1021 35 88 26 77 47 55 57 33 2 2 19 5 36 21
2011 29 84 50 40 54 53 63 54 1 2 35 6 19 15
1001 16 69 18 40 59 25 50 54 2 1 18 4 5 12
0000 13 45 10 49 47 4 54 54 2 2 6 3 0 5
1121 12 83 40 60 46 41 48 31 2 2 24 12 40 17
2120 10 69 82 71 46 57 55 37 2 1 49 16 34 6
1111 8 82 30 29 60 41 53 38 3 2 25 10 18 16
1022 7 97 7 85 48 64 18 39 2 2 13 4 40 33
2021 6 87 62 56 62 57 53 51 1 3 38 6 33 14
1110 5 55 56 72 58 51 55 38 4 2 26 12 16 6
1020 5 62 46 87 51 24 43 18 2 1 20 5 32 8
1100 4 29 54 68 46 29 44 44 4 2 22 11 2 2
2200 4 38 95 74 46 36 36 54 4 3 67 34 4 3
2210 3 67 95 72 45 41 20 52 4 2 62 31 23 5
0001 3 79 10 87 64 9 65 73 3 0 8 4 5 15
0011 3 78 14 92 49 22 74 67 0 3 8 0 18 18
2221 2 92 91 54 11 49 12 54 4 1 58 30 38 12
2020 2 70 89 98 54 34 3 46 0 3 65 3 46 6
2220 1 71 99 77 67 63 27 16 5 5 55 33 33 8
1101 1 89 40 18 31 1 68 22 5 5 27 12 7 14
2101 1 93 79 66 75 0 77 97 4 1 53 22 7 12
  1. In this particular experiment, ECM, EGF, ExtPump, alpha_q, alpha_i, and alpha_12_13 ligands were set to vary between 0–100% ON, while IL1_TNF and Stress varied between 0 and 5% ON. The first and second columns summarize all global outputs (or patterns) and their frequency produced by the model in response to the various external stimuli. Columns labeled as Average Inputs represent all external inputs and their average % ON value for a given global output. Similarly, Average Outputs contain output nodes and their average % ON for a given pattern. In this example the patterns are in ternary: 0–9% ON = 0, 10–29% ON = 1, and 30–100% ON = 2. These ranges were determined to be the most useful in previous experiments [14], but any ranges (or discretization) can be used. Focusing on the first row, it can be seen that there were 218 of the 1000 simulations where output pattern was '1000', i.e., Akt output was in the 10–29% range, Erk was in the 0–9% range, etc. Of those 218 simulations, the average output values of Akt was 20, the average Erk value was 3, etc. The average external-input values that elicited the '1000' response is given in each of the Inputs columns, e.g., the average external-input value that resulted in the '1000' response was ECM = 23% ON, EGF = 26% ON, etc. These experiments were carried out under non-stress conditions, thus IL1_TNF and Stress external inputs varied only from 0 to 5% ON.