Table 4 Genome wide analysis. Connected components' scores before and after resolving conflicts. For each component we list the names of the constituent pathways, the number of conflicts (shared assignments) and the component score. Note that not all conflicts are solvable. For example, the first connected component contains three pathways, and the best initial assignment results in 6 conflicts. Of these only two are solvable (i.e. there are multiple enzymes that can be assigned to these reactions). The final assignment resolves these conflicts while reducing the score of the connected component only slightly (9.31 compared to 10.22).
From: Automation of gene assignments to metabolic pathways using high-throughput expression data
Component Number | Pathways | Number of Conflicts (solvable conflicts) | Component score | ||
|---|---|---|---|---|---|
| Â | Â | Before | After | Before | After |
1 | isoleucine biosynthesis I valine biosynthesis leucine biosynthesis | 6(2) | 4 | 10.22 | 9.31 |
2 | aerobic glycerol degradation II glycolysis | 5(3) | 2 | 7.58 | 7.22 |
3 | asparagine biosynthesis I glutamate – aspartate pathway glutamate degradation VI aspartate biosynthesis II aspartate biosynthesis and degradation | 4(0) | 4 | 6.82 | 6.82 |
4 | trehalose anabolism galactose metabolism UDP-glucose conversion trehalose biosynthesis | 4(1) | 3 | 6.64 | 6.62 |
5 | pentose phosphate pathway, Mycoplasma pneumoniae ribose degradation non-oxidative branch of the pentose phosphate pathway | 5(2) | 3 | 5.60 | 4.78 |
6 | serine biosynthesis cysteine biosynthesis II | 3(0) | 3 | 3.98 | 3.98 |
7 | glycine biosynthesis I glycine cleavage folic acid biosynthesis | 3(2) | 1 | 3.41 | 3.41 |
8 | arginine biosynthesis, Bacillus subtilis de novo biosynthesis of pyrimidine ribonucleotides | 0(0) | 0 | 2.08 | 2.08 |
9 | alanine degradation 3 alanine biosynthesis II | 1(1) | 0 | 0 | 0 |
10 | phenylalanine biosynthesis I tyrosine biosynthesis I | 2(1) | 1 | -1.31 | -1.33 |