Table 1.
Proportion of pathways from CPDB databases
| Median size | CPDB % | Standard set cover | Hitting set cover | Proportional set cover | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 100% | 99% | 95% | 90% | 100% | 99% | 95% | 90% | 100% | 99% | 95% | 90% | |||
| BioCarta | 15.0 | 6.3 | 6.3 | 4.6 | 0.5 | 0.0 | 4.7 | 4.8 | 5.4 | 5.4 | 5.8 | 6.1 | 6.1 | 5.0 |
| EHMN | 32.5 | 1.6 | 3.2 | 3.4 | 2.6 | 1.0 | 2.1 | 2.3 | 1.8 | 1.6 | 1.6 | 1.4 | 0.9 | 0.9 |
| HumanCyc | 5.0 | 8.2 | 6.5 | 7.7 | 2.6 | 0.0 | 10.1 | 10.9 | 12.9 | 14.3 | 10.9 | 11.7 | 13.7 | 15.4 |
| INOH | 34.5 | 2.3 | 1.7 | 1.9 | 1.0 | 1.0 | 0.8 | 0.6 | 0.3 | 0.2 | 1.1 | 1.1 | 0.9 | 0.7 |
| KEGG | 65.0 | 7.2 | 29.0 | 30.5 | 37.6 | 40.4 | 15.8 | 15.0 | 13.5 | 13.4 | 12.2 | 9.9 | 8.3 | 7.1 |
| NetPath | 51.0 | 0.9 | 2.1 | 2.4 | 3.6 | 5.1 | 1.1 | 1.2 | 1.1 | 1.0 | 1.0 | 0.9 | 0.6 | 0.2 |
| PharmGKB | 13.0 | 2.8 | 3.1 | 2.9 | 0.5 | 0.0 | 2.0 | 2.1 | 2.4 | 2.3 | 2.1 | 2.2 | 2.1 | 1.7 |
| PID | 35.0 | 5.2 | 15.6 | 13.9 | 10.3 | 6.1 | 9.5 | 9.8 | 9.4 | 8.5 | 8.2 | 8.3 | 6.4 | 4.6 |
| Reactome | 17.0 | 39.6 | 4.2 | 5.3 | 10.8 | 21.2 | 36.1 | 35.1 | 34.7 | 35.3 | 39.4 | 40.9 | 45.1 | 48.8 |
| Signalink | 32.0 | 0.4 | 1.0 | 1.2 | 1.0 | 0.0 | 0.6 | 0.7 | 0.7 | 0.7 | 0.7 | 0.7 | 0.7 | 0.8 |
| SMPDB | 11.0 | 16.7 | 1.7 | 1.4 | 0.5 | 0.0 | 1.6 | 1.5 | 1.4 | 1.2 | 2.8 | 3.0 | 2.9 | 3.2 |
| Wikipathways | 26.0 | 8.8 | 25.6 | 24.9 | 28.9 | 25.3 | 15.6 | 16.0 | 16.2 | 16.2 | 14.2 | 13.7 | 12.5 | 11.7 |
Median size represents the median sizes of the pathways in the CPDB dataset. CPDB % represents the proportion of the pathways in the unaltered dataset that came from each database. The following columns represent the proportion of pathways in the set cover generated by the standard set cover algorithm, the hitting set cover algorithm and the proportional set cover algorithm. Different results are obtained by altering the proportion of the gene set covered, shown in subcolumns below the algorithm header