Supplementary Information for SAGPAR

This material includes testing results of SAGPAR on all the 49 pathway data-sets of Homo sapiens and Mycoplasma pneumoniae M129.

Index

  1. List of non-pool metabolites: Section A (Page 2)
  2. List of pool metabolites: Section B (Page 2)
  3. Calculating threshold value for arginine, proline metabolism in M. pneumoniae M129: Section C (Page 3)
  4. Legends in figures: Section D (Page 3)
  5. Pathway reconstruction in Homo sapiens: Figs 4-27 (Pages 4-27)
  6. Pathway reconstruction in M. pneumoniae M129: Figs 28-52 (Pages 5-52)
  7. Nodes and edge prediction using SAGPAR in pathways of Homo sapiens: Table 1 (Page 53)
  8. Nodes and edge prediction using SAGPAR in pathways of M. pneumonia M129: Table 2 (Page 54)
  9. Pool prediction using SAGPAR in pathways of Homo sapiens: Table 3 (Page 55)
  10. Pool prediction using SAGPAR in pathways of M. pneumonia M129: Table 4 (Page 56)
  11. Range of T-value in pathways of Homo sapiens: Table 5 (Page 57)
  12. Range of T-value in pathways of M. pneumonia M129: Table 6 (Page 58)
  13. Comparison of SAGPAR with Jarnac, PHT, Gepasi, Copasi and Path-A in pathways of M. pneumoniae M129: Table 7 (Page 59)
  14. Comparison of SAGPAR with Jarnac, PHT, Gepasi, Copasi and Path-A in pathways of H. sapiens: Table 8 (Page 60)

Section A.

Non-pool metabolites

1.  L-erythro-4-hydroxyglutamate {(1): C( C( C( =O )O )N )C( C( =O )O )O}

2.  N-carbamoyl-sarcosine {(2): CN( CC( =O )O )C( =O )N}

3.  Carbamoyl-P {(3): C( =O )( N )OP( =O )( O )O}

4.  L-citrulline {(4): C( CC( C( =O )O )N )CNC( =O )N}

5.  L-arginine {(5): C( CC( C( =O )O )N )CN=C( N )N}

6.  L-arginyl-tRNA ( Arg ) {(6): C( CC( C( =O )N )CN=C( N )N( O )O )C}

7.  L-ornithine {(7): C( CC( C( =O )O )N )CN}

8.  Trans-4-hydroxy-L-proline {(8): C( CC( C( =O )O )N )CCN}

9.  L-glutamate {(9): C( CC( =O )[O-] )C( C( =O )[O-] )[NH3+]}

10.  L-glutamate-semialdehyde {(10): C( CC( =O )[O-] )C( CC( =O )O[O-] )[NH3+]}

11.  L-1-pyrroline-3-hydroxy-5-carboxylate {(11): C1C( C=NC1C( =O )O )O}

12.  L-prolyl-tRNA {(12): C1CC( NC1 )CC( =O )O}

13.  L-Proline {(13): C1CC( NC1 )C( =O )O}

Section B.

Pool metabolites

1.  NADPH {(p1): C1C=CN( C=C1C( =O )N )C2C( C( C( O2 )COP( =O )( O )OP( =O )( O )OCC3C( C( C( O3 )N4C=NC5}

2.  O {(p2): O}

3.  H {(p3:) H}

4.  ATP {(p4): C1=NC2=C( C( =N1 )N )N=CN2C3C( C( C( O3 )COP( =O )( O )OP( =O )( O )OP( =O )( O )O )O )O}

5.  NH3 {(p5): N}

6.  CO2 {(p6): OCO}

7.  ADP {(p7): C1=NC2=C( C( =N1 )N )N=CN2C3C( C( C( O3 )COP( =O )( O )OP( =O )( O )O )O )O}

8.  NADP+ {(p8): C1=CC( =C[N+]( =C1 )C2C( C( C( O2 )COP( =O )( [O-] )OP( =O )( [O- )OCC3C( C( C( O3 )N4C=NC5=C4N=CN=C5N )OP( =O )[O-] )[O-] )O )O )O )C}

  1. NO2 {(p9): ONO}
  2. H2O {(p10): HOH}

Section C.

Calculating threshold value for arginine, proline metabolism in M. pneumoniae M129

T = 0.32, the scoring pairs are 1-3, 1-5, 1-6, 1-7, 2-3, 2-4, 2-6, 2-8, 2-9, 3-4, 3-5, 3-6, 3-8, 4-1, 4-6, 5-6, 5-9, 5-10, 7-10, 7-12, 7-13, 9-10, 9-11 and 11-13.

T = 0.38, the scoring pairs are 1-5, 1-6, 1-7, 2-3, 2-6, 2-9, 3-4, 3-5, 3-6, 3-8, 4-1, 4-5, 4-6, 5-6, 5-9, 5-10, 7-10, 7-12, 7-13, 9-10, 9-11 and 11-13.

T = 0.42, the scoring pairs are 1-4, 1-5, 1-6, 1-7, 2-3, 2-6, 2-9, 3-4, 3-5, 3-6, 3-8, 4-5, 4-6, 5-6, 5-9, 5-10, 7-10, 7-12, 7-13, 9-10, 9-11 and 11-13.

T = 0.44, the scoring pairs are 1-4, 1-5, 2-3, 2-6, 3-4, 3-5, 3-6, 4-5, 4-6, 5-6, 5-9, 5-10, 7-10, 7-12, 7-13, 9-10, 10-11, 11-13 and 12-13.

T = 0.47, the scoring pairs are 1-4, 1-5, 2-3, 2-6, 3-4, 3-5, 3-6, 4-5, 4-6, 5-6, 5-9, 7-10, 7-12, 7-13, 9-10, 10-11, 11-13 and 12-13.

T = 0.50, the scoring pairs are 1-4, 1-5, 2-3, 3-4, 3-5, 3-6, 4-5, 4-6, 5-6, 7-10, 7-13, 9-10, 9-11, 10-11, 11-13 and 12-13.

T = 0.52, the scoring pairs are 1-4, 1-5, 2-3, 3-4, 3-5, 3-6, 4-5, 4-6, 5-6, 7-10, 7-13, 9-11, 10-11, 11-13 and 12-13. MINIMA

T = 0.55, the scoring pairs are 1-4, 2-3, 3-4, 3-9, 4-5, 4-7, 5-6, 7-10, 9-11, 10-11, 11-13 and 12-13. SELECTED ‘T-value’

T = 0.57, the scoring pairs are 1-4, 2-3, 3-4, 3-9, 4-5, 5-6, 7-10, 9-11, 10-11, 11-13 and 12-13.

T = 0.59, the scoring pairs are 1-4, 2-3, 3-4, 3-9, 4-5, 5-6, 7-10, 9-11, 10-11, 11-13 and 12-13.

T = 0.61, the scoring pairs are 1-4, 2-3, 3-4, 4-5, 5-6, 7-10, 9-11, 10-11, 11-13 and 12-13.

T = 0.63, the scoring pairs are 2-3, 3-4, 4-5, 5-6, 7-10, 9-11, 10-11, 11-13 and 12-13. MAXIMA

T = 0.66, the scoring pairs are 4-5, 5-6, 7-10, 9-11, 10-11 and 12-13.

T = 0.68, the scoring pairs are 5-6, 9-11, 10-11 and 12-13.

T = 0.69, the scoring pairs are 5-6, 9-11 and 12-13.

T = 0.71, the scoring pairs are 12-13.

Section D

Legends in figures

  1. ‘ ? ’ and ‘------’ : Unrecognized edge / reaction link
  2. ‘ X ’ : Wrong edge / reaction link
  3. ‘ ’ : Correct edge / reaction link

Fig. 4. Reconstruction of Pentose Phosphate Pathway in Homo sapiens

Fig. 5. Reconstruction of Pentose & Glucoronate Interconversion in Homo sapiens

Fig. 6. Reconstruction of Fructose & Mannose Metabolism in Homo sapiens

Fig. 7. Reconstruction of Galactose Metabolism in Homo sapiens

Fig. 8. Reconstruction of Asorbate & Aldarate Metabolism in Homo sapiens

Fig. 9. Reconstruction of Starch & Sucrose Metabolism in Homo sapiens

Fig. 10. Reconstruction of Pyruvate Metabolism in Homo sapiens

Fig. 11. Reconstruction of Biosynthesis of Steroids in Homo sapiens

Fig. 12. Reconstruction of Purine Metabolism in Homo sapiens

Fig. 13. Reconstruction of Pyrimidine Metabolism in Homo sapiens

Fig. 14. Reconstruction of Alanine & Aspartate Metabolism in Homo sapiens

Fig. 15. Reconstruction of Glycine, Serine & Threonine Metabolism in Homo sapiens

Fig. 16. Reconstruction of Methionine Metabolism in Homo sapiens

Fig. 17. Reconstruction of Valine, Leucine & Isoleucine Degradation in Homo sapiens

Fig. 18. Reconstruction of Valine, Leucine & Isoleucine Biosynthesis in Homo sapiens

Fig. 19. Reconstruction of Arginine & Proline Metabolism in Homo sapiens

Fig. 20. Reconstruction of Tyrosine Metabolism in Homo sapiens

Fig. 21. Reconstruction of Tryptophan Metabolism in Homo sapiens

Fig. 22. Reconstruction of Phenylalanine, Tyrosine & Tryptophan Biosynthesis in Homo sapiens

Fig. 23. Reconstruction of Glutamate Metabolism in Homo sapiens

Fig. 24. Reconstruction of Lysine Biosynthesis in Homo sapiens

Fig. 25. Reconstruction of Porphyrin Metabolism in Homo sapiens

Fig. 26. Reconstruction of Drug Metabolism - Cytochrome P450 in Homo sapiens

Fig. 27. Reconstruction of Metabolism of Xenobiotics by Cytochrome P450 in Homo sapiens

Fig. 28. Reconstruction of Glycolysis in Mycoplasma pneuminiae M129

Fig. 29. Reconstruction of Pentose Phosphate Pathway in Mycoplasma pneuminiae M129

Fig. 30. Reconstruction of Pentose & Glucoronate Interconversion in Mycoplasma pneuminiae M129

Fig. 31. Reconstruction of Fructose & Mannose Metabolism in Mycoplasma pneuminiae M129

Fig. 32. Reconstruction of Galactose Metabolism in Mycoplasma pneuminiae M129

Fig. 33. Reconstruction of Asorbate & Aldarate Metabolism in Mycoplasma pneuminiae M129

Fig. 34. Reconstruction of Starch & Sucrose Metabolism in Mycoplasma pneuminiae M129

Fig. 35. Reconstruction of Pyruvate Metabolism in Mycoplasma pneuminiae M129

Fig. 36. Reconstruction of Glycerophospholipid Metabolism in Mycoplasma pneuminiae M129

Fig. 37. Reconstruction of Purine Metabolism in Mycoplasma pneuminiae M129

Fig. 38. Reconstruction of Pyrimidine Metabolism in Mycoplasma pneuminiae M129

Fig. 39. Reconstruction of Glutamate Metabolism in Mycoplasma pneuminiae M129

Fig. 40. Reconstruction of Alanine & Aspartate Metabolism in Mycoplasma pneuminiae M129

Fig. 41. Reconstruction of Glycine, Serine & Threonine Metabolism in Mycoplasma pneuminiae M129

Fig. 42. Reconstruction of Methionine Metabolism in Mycoplasma pneuminiae M129

Fig. 43. Reconstruction of Valine, Leucine & Isoleucine Degradation in Mycoplasma pneuminiae M129

Fig. 44. Reconstruction of Valine, Leucine & Isoleucine Biosynthesis in Mycoplasma pneuminiae M129

Fig. 45. Reconstruction of Arginine & Proline Metabolism in Mycoplasma pneuminiae M129

Fig. 46. Reconstruction of Phenylalanine, Tyrosine & Tryptophan Biosynthesis in Mycoplasma pneuminiae M129

Fig. 47. Reconstruction of Selenoamino acid in Mycoplasma pneuminiae M129

Fig. 48. Reconstruction of Glutathione Metabolism in Mycoplasma pneuminiae M129

Fig. 49. Reconstruction of Thiamine Metabolism in Mycoplasma pneuminiae M129

Fig. 50. Reconstruction of Riboflavin Metabolism in Mycoplasma pneuminiae M129

Fig. 51. Reconstruction of Pantothenate & CoA Biosynthesis in Mycoplasma pneuminiae M129

Fig. 52. Reconstruction of Folate Biosynthesis in Mycoplasma pneuminiae M129

Table 1. Nodes and edge prediction using SAGPAR in pathways of H. sapiens

Pathway / #Nodes in repository / #Edges in repository / #Correct Nodes / #Correct Edges / #Wrong Edge / #Unrecognized
Edge
1 / Pentose Phosphate Pathway / 33 / 21 / 32 / 20 / 0 / 1
2 / Pentose & Glucoronate Interconversion / 53 / 19 / 52 / 18 / 1 / 1
3 / Fructose & Mannose Metabolism / 42 / 22 / 40 / 20 / 0 / 2
4 / Galactose Metabolism / 40 / 23 / 39 / 22 / 1 / 1
5 / Asorbate & Aldarate Metabolism / 47 / 11 / 47 / 11 / 1 / 0
6 / Starch & Sucrose Metabolism / 44 / 33 / 43 / 32 / 0 / 1
7 / Pyruvate Metabolism / 29 / 23 / 28 / 22 / 1 / 1
8 / Biosynthesis of Steroids / 75 / 47 / 73 / 45 / 0 / 2
9 / Purine Metabolism / 86 / 83 / 84 / 80 / 2 / 3
10 / Pyrimidine Metabolism / 56 / 64 / 55 / 62 / 0 / 2
11 / Alanine & Aspartate Metabolism / 24 / 22 / 23 / 22 / 1 / 0
12 / Glycine, Serine & Threonine Metabolism / 44 / 36 / 42 / 35 / 1 / 1
13 / Methionine Metabolism / 27 / 14 / 26 / 14 / 1 / 0
14 / Valine, Leucine & Isoleucine Degradation / 35 / 40 / 34 / 38 / 0 / 2
15 / Valine, Leucine & Isoleucine Biosynthesis / 28 / 20 / 27 / 19 / 1 / 1
16 / Arginine & Proline Metabolism / 46 / 26 / 45 / 25 / 1 / 1
17 / Tyrosine Metabolism / 82 / 54 / 81 / 52 / 1 / 2
18 / Tryptophan Metabolism / 78 / 38 / 76 / 36 / 0 / 2
19 / Phenylalanine, Tyrosine & Tryptophan Biosynthesis / 23 / 16 / 22 / 16 / 1 / 0
20 / Glutamate Metabolism / 24 / 17 / 24 / 16 / 0 / 1
21 / Lysine Biosynthesis / 31 / 16 / 30 / 16 / 1 / 0
22 / Porphyrin Metabolism / 93 / 40 / 91 / 39 / 1 / 1
23 / Drug Metabolism - Cytochrome P450 / 87 / 44 / 85 / 43 / 1 / 1
24 / Metabolism of Xenobiotics by Cytochrome P450 / 81 / 36 / 79 / 35 / 0 / 1

Table 2. Nodes and edge prediction using SAGPAR in pathways of M. pneumonia M129

Pathway / #Nodes in repository / #Edges in repository / #Correct Nodes / #Correct Edges / #Wrong Edge / #Unrecognized Edge
1 / Glycolysis / 12 / 11 / 11 / 10 / 0 / 1
2 / Pentose Phosphate Pathway / 13 / 12 / 12 / 11 / 1 / 0
3 / Pentose & Glucoronate Interconversion / 14 / 12 / 14 / 11 / 0 / 0
4 / Fructose & Mannose Metabolism / 13 / 12 / 13 / 11 / 0 / 0
5 / Galactose Metabolism / 11 / 10 / 10 / 9 / 0 / 2
6 / Asorbate & Aldarate Metabolism / 10 / 9 / 10 / 8 / 0 / 0
7 / Starch & Sucrose Metabolism / 13 / 12 / 12 / 11 / 1 / 1
8 / Pyruvate Metabolism / 13 / 14 / 13 / 12 / 0 / 0
9 / Glycerophospholipid Metabolism / 11 / 11 / 11 / 10 / 0 / 0
10 / Purine Metabolism / 30 / 30 / 29 / 28 / 0 / 2
11 / Pyrimidine Metabolism / 24 / 22 / 23 / 20 / 1 / 2
12 / Glutamate Metabolism / 10 / 8 / 10 / 8 / 0 / 0
13 / Alanine & Aspartate Metabolism / 10 / 7 / 10 / 6 / 0 / 0
14 / Glycine, Serine & Threonine Metabolism / 8 / 5 / 8 / 4 / 0 / 0
15 / Methionine Metabolism / 7 / 5 / 7 / 5 / 0 / 0
16 / Valine, Leucine & Isoleucine Degradation / 16 / 15 / 15 / 14 / 1 / 1
17 / Valine, Leucine & Isoleucine Biosynthesis / 17 / 13 / 16 / 11 / 0 / 2
18 / Arginine & Proline Metabolism / 13 / 12 / 12 / 11 / 0 / 1
19 / Phenylalanine, Tyrosine & Tryptophan Biosynthesis / 7 / 5 / 7 / 5 / 0 / 0
20 / Selenoamino acid / 7 / 7 / 7 / 6 / 0 / 0
21 / Glutathione Metabolism / 13 / 11 / 12 / 10 / 1 / 1
22 / Thiamine Metabolism / 14 / 10 / 13 / 9 / 1 / 1
23 / Riboflavin Metabolism / 11 / 9 / 11 / 9 / 0 / 0
24 / Pantothenate & CoA Biosynthesis / 7 / 7 / 7 / 6 / 0 / 0
25 / Folate Biosynthesis / 13 / 13 / 12 / 12 / 1 / 1

Table 3. Pool prediction using SAGPAR in pathways of H. sapiens