Table 1 Summary of pathway assignments. For each pathway in the test set we report the number of reactions, the number of assignments considered, the number of curated (SGD verified) assignments, and the maximal and minimal assignment scores. The score reported is the weighted average score per pair of compared enzymes. The score reflects the average significance of a pairwise relation within a pathway. The larger the score the more significant is the relation. Negative scores suggest anti-correlation and near-zero scores provide no evidence that the two genes are related. Pathways are sorted based on assignment score.
From: Automation of gene assignments to metabolic pathways using high-throughput expression data
Pathway | Number of reactions | Number of assignments | Number of curated assignments | Max(Min) Score Normalized |
|---|---|---|---|---|
methionine and S-adenosylmethionine synthesis | 2 | 2 | 2 | 10.45 (7.34) |
isoleucine biosynthesis I | 5 | 12 | 4 | 10.32 (3.00) |
leucine biosynthesis | 4 | 4 | 4 | 10.08 (4.01) |
valine biosynthesis | 4 | 4 | 4 | 10.14 (4.99) |
asparagine biosynthesis I | 2 | 4 | 4 | 8.80 (-4.88) |
proline biosynthesis I | 3 | 1 | 1 | 8.43 (8.43) |
homoserine methionine biosynthesis | 2 | 1 | 1 | 7.33 (7.33) |
tryptophan biosynthesis | 5 | 2 | 2 | 5.29 (4.13) |
aspartate biosynthesis II | 2 | 4 | 4 | 4.85 (0.75) |
non-oxidative branch of the pentose phosphate pathway | 5 | 8 | 8 | 4.82 (0.84) |
folic acid biosynthesis | 11 | 48 | 32 | 4.63 (1.26) |
glutamate biosynthesis I | 2 | 2 | 2 | 4.08 (-4.88) |
glutathione biosynthesis | 2 | 1 | 1 | 4.03 (4.03) |
glutamate degradation VIII | 5 | 1 | 1 | 3.92 (3.92) |
serine biosynthesis | 3 | 2 | 2 | 3.58 (-0.58) |
purine biosynthesis 2 | 14 | 16 | 8 | 2.50 (2.06) |
homocysteine and cysteine interconversion | 3 | 2 | 1 | 2.35 (2.01) |
biotin biosynthesis I | 3 | 1 | 1 | 2.27 (2.27) |
homocysteine degradation I | 2 | 1 | 1 | 2.01 (2.01) |
threonine biosynthesis from homoserine | 2 | 1 | 1 | 0.87 (0.87) |
glutamine – glutamate pathway II | 1 | 1 | 1 | 0.00 (0.00) |
tyrosine biosynthesis I | 3 | 2 | 2 | -0.53 (-0.58) |
glycine biosynthesis I | 2 | 2 | 2 | -0.91 (-3.60) |
phenylalanine biosynthesis I | 3 | 2 | 2 | -2.09 (-2.80) |