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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.