Method | Enriched Clusters | # NEC | % NEC | # NEC S | % NEC S |
---|
PPI | 8/19 (42.11%) | 280.0 | 4.59% | 226.0 | 3.71% |
3.5 | 63/105 (60.00%) | 504.0 | 8.27% | 464.0 | 7.61% |
4.0 | 128/189 (67.72%) | 1108.0 | 18.18% | 919.0 | 15.08% |
4.5 | 207/311 (66.56%) | 1951.0 | 32.00% | 1430.0 | 23.46% |
5.0 | 153/303 (50.50%) | 2476.0 |
40.62%
| 1531.0 |
25.11%
|
5.5 | 70/164 (42.68%) | 2418.0 | 39.67% | 1269.0 | 20.82% |
6.0 | 43/88 (48.86%) | 1398.0 | 22.93% | 837.0 | 13.73% |
- NEC= “Nodes in Enriched Clusters”. We calculate %NEC in two settings: %NEC is enrichment in the GO hierarchy with terms above the fifth level filtered out, and %NEC S uses the same filtered GO hierarchy, but then only gives a node credit if there is a match between one of the node’s labels and one of the terms for which there is GO enrichment for the cluster. Walktrap run alone produces a very small number of clusters; because of this only the S statistic is meaningful to compare the DSD versions against unmodified Walktrap. Walktrap with DSD at thresholds between 4.5 and 6 trade a larger number of smaller clusters for a lower percentage of nodes in enriched clusters
- Bolded values represent the best values achieved for the %NEC and %NEC S statistics comparing the PPI network and different DSD detangling thresholds