Reference pathway processing

Reference pathways were extracted from the aMAZE database in September 2006. Details on the pathways are given in the table below.

OrganismsE. coliS. cerevisiaeH.sapiens
Pathways before filtering
Pathways (116)552932
Cyclic pathways (7)241
Branched pathways (25)1357
Pathways with less than 3 reactions (46)201412
Pathways after filtering and linearization
Pathways (69)371418

E. coli

Reference pathways

For E. coli, path finding accuracy has been benchmarked against 37 reference pathways. 32 of them were considered for accuracy calculation, because 5 pathways contain reactions that could not be mapped to reactant pairs. This affects the following pathways:
The distribution of the pathway length of the 37 pathways is shown here. In average, the pathways have 8 nodes.

Path finding accuracy

Table S5 (supplementary material) as simple tab-delimited text file. Complete evaluation results for 104 experiments with 32 reference pathways.
The table is available here.

S. cerevisiae

Reference pathways

For S. cerevisiae, path finding accuracy has been benchmarked against 14 reference pathways. 11 of them were considered for accuracy calculation, because 3 pathways contain reactions that could not be mapped to reactant pairs. This affects the following pathways:
The distribution of the pathway length of the 14 pathways is shown here. In average, the pathways have 13 nodes.

Path finding accuracy

Table S6 (supplementary material) as simple tab-delimited text file. Complete evaluation results for 104 experiments with 11 reference pathways.
The table is available here.

Homo sapiens

Reference pathways

For Homo sapiens, path finding accuracy has been benchmarked against 18 reference pathways. 12 of them were considered for accuracy calculation, because 6 pathways contain reactions that could not be mapped to reactant pairs. This affects the following pathways:
The distribution of the pathway length of the 18 pathways is shown here. In average, the pathways have 14 nodes. The two pathways:
BileacidSynthesis-Human.gdl-R01463-R03975
BileacidSynthesis-Human.gdl-R01463-R03977
have not been found in RPAIR graphs including all or main-trans reactant pair classes.

Path finding accuracy

Table S7 (supplementary material) as simple tab-delimited text file. Complete evaluation results for 104 experiments with 12 reference pathways.
The table is available here.

Reference organisms merged

Table S8 (supplementary material) lists the complete evaluation results for all three organisms merged as simple tab-delimited text file.
The table is available here.

Wilcoxon tables

Table T3 lists the results for experiment-wise Wilcoxon pair-wise signed rank test for the default scoring scheme.
Table T3
Table S9 lists the results for the same test using the alternative scoring scheme (alternative reactions between two compounds are not counted as false positive).
Table S9

Table T4 shows the results for the best-combination-wise Wilcoxon pair-wise signed rank test for the default scoring scheme.
Table T4
Table S10 shows the results for the same test using the alternative scoring scheme.
Table S10