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Table 5 Genome wide analysis. Statistics of the final assignments. For each pathway we list the number of possible assignments, the maximum and minimum scores observed over these assignments, and the final score (note that the final score might not be the maximum score, due to conflicts that were resolved at the refinement stage). The last column gives the number of pairwise relations considered in each assignment, and the number of negative-scoring pairs in the final assignment (in parentheses). Negative scores indicate anti or no correlation. Pathways are sorted by the final assignment score. Note that most pathways are assigned a high positive score, and almost all pairs in the final assignments are positive pairs.

From: Automation of gene assignments to metabolic pathways using high-throughput expression data

Pathway Number of Assignments Max Score Min Score Final Score Number of pairs (negative Pairs)
pentose phosphate pathway, Mycoplasma pneumoniae 2 11.03 -0.73 11.03 1(0)
sulfate assimilation 2 1 11.02 11.02 11.02 1(0)
methionine and S-adenosylmethionine synthesis 2 10.45 7.34 10.45 1(0)
isoleucine biosynthesis I 12 10.32 3.00 10.32 10(0)
valine biosynthesis 4 10.14 4.99 10.14 6(0)
trehalose biosynthesis 2 10.02 9.65 9.65 1(0)
glutamate degradation I 1 9.64 9.64 9.64 3(0)
arginine biosynthesis I 1 9.58 9.58 9.58 3(0)
chorismate biosynthesis 2 9.24 8.19 9.24 21(0)
glycolysis 180 8.98 3.16 8.87 28(0)
asparagine biosynthesis I 4 8.80 -4.88 8.80 1(0)
trehalose anabolism 8 8.80 0.27 8.80 6(0)
proline biosynthesis I 1 8.43 8.43 8.43 3(0)
galactose metabolism 4 7.91 4.62 7.91 6(0)
glycine degradation III 2 7.73 7.73 7.73 1(0)
methylglyoxal degradation 2 7.59 0.98 7.59 1(0)
tRNA charging pathway 49152 7.41 1.69 7.41 171 (2)
glyoxylate cycle 72 7.37 0.27 7.37 10(0)
homoserine methionine biosynthesis 1 7.33 7.33 7.33 1(0)
pyruvate dehydrogenase 2 6.43 4.33 6.43 1(0)
removal of superoxide radicals 4 5.93 -0.45 5.93 1(0)
aerobic glycerol degradation II 180 6.19 1.64 5.58 28(1)
aspartate biosynthesis II 4 4.85 0.75 4.85 1(0)
non-oxidative branch of the pentose phosphate pathway 8 4.82 0.84 4.82 10(1)
oxidative branch of the pentose phosphate pathway 6 4.78 1.07 4.78 3(0)
arginine biosynthesis, Bacillus subtilis 3 4.55 2.69 4.55 34(4)
leucine biosynthesis 4 10.08 4.01 4.31 3(0)
UDP-N-acetylglucosamine biosynthesis 1 4.22 4.22 4.22 1(0)
cysteine biosynthesis II 2 4.19 0.94 4.19 6(0)
tryptophan biosynthesis 2 4.13 3.99 4.13 10(1)
glutamate biosynthesis I 2 4.08 -4.88 4.08 1(0)
glutathione biosynthesis 1 4.03 4.03 4.03 1(0)
arginine degradation I 1 4.00 4.00 4.00 3(0)
arginine proline degradation 1 3.84 3.84 3.84 3(0)
serine biosynthesis 2 3.58 -0.58 3.58 3(0)
folic acid biosynthesis 48 3.49 0.23 3.49 55 (12)
histidine biosynthesis I 1 2.48 2.48 2.48 12(2)
purine biosynthesis 2 16 2.43 2.01 2.43 90 (27)
homocysteine and cysteine interconversion 2 2.35 2.01 2.35 3(1)
biotin biosynthesis I 1 2.27 2.27 2.27 3(2)
homocysteine degradation I 1 2.01 2.01 2.01 1(0)
glutamate degradation VIII 1 1.86 1.86 1.86 8(2)
homoserine biosynthesis 1 1.14 1.14 1.14 3(1)
threonine biosynthesis from homoserine 1 0.87 0.87 0.87 1(0)
de novo biosynthesis of pyrimidine ribonucleotides 12 0.14 -0.69 0.14 43 (25)
ornithine spermine biosynthesis 2 -0.24 -2.48 -0.24 3(2)
tyrosine biosynthesis I 2 -0.53 -0.58 -0.58 3(1)
glycine biosynthesis I 2 -0.91 -3.60 -0.91 1(1)
UDP-glucose conversion 4 -1.32 -2.04 -1.32 3(2)
ribose degradation 2 8.06 -1.74 -1.74 1(1)
phenylalanine biosynthesis I 2 -2.09 -2.80 -2.09 3(2)
tryptophan kynurenine degradation 1 -2.46 -2.46 -2.46 1(1)