Method | Enriched Clusters | # NEC | % NEC | # NEC S | % NEC S |
---|
PPI | 35/64 (54.69%) | 3274.0 | 53.69% | 1703.0 | 27.93% |
3.5 | 56/91 (61.54%) | 570.0 | 9.35% | 468.0 | 7.68% |
4.0 | 97/142 (68.31%) | 1155.0 | 18.95% | 915.0 | 15.01% |
4.5 | 144/215 (66.98%) | 1869.0 | 30.66% | 1415.0 | 23.21% |
5.0 | 96/174 (55.17%) | 2785.0 | 45.69% | 1724.0 | 28.28% |
5.5 | 56/93 (60.22%) | 4067.0 | 66.72% | 1783.0 |
29.25%
|
6.0 | 51/81 (62.96%) | 4155.0 |
68.16%
| 1667.0 | 27.35% |
PPI | 39/69 (56.52%) | 3367.0 | 55.21% | 1782.0 | 29.22% |
3.5 | 55/91 (60.44%) | 495.0 | 8.12% | 463.0 | 7.60% |
4.0 | 97/142 (68.31%) | 1155.0 | 18.95% | 915.0 | 15.01% |
4.5 | 144/215 (66.98%) | 1869.0 | 30.66% | 1415.0 | 23.21% |
5.0 | 95/174 (54.60%) | 2686.0 | 44.06% | 1676.0 | 27.49% |
5.5 | 60/106 (56.60%) | 3978.0 | 65.26% | 1862.0 |
30.54%
|
6.0 | 66/96 (68.75%) | 4077.0 |
66.88%
| 1680.0 | 27.56% |
- The numbers above the double line are for cutting the Walktrap dendrogram at 200 clusters; the numbers below the double line are for cutting the Walktrap dendrogram at 300 clusters. 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. In both cases, for the S statistic the best DSD threshold is 5.5, at which performance is slightly better than running Walktrap directly on the PPI network. For cutoffs of both 200 and 300 nodes, DSD+Walktrap is slightly better than Walktrap in the NEC measure, and in both cases the DSD version produces slightly more and smaller clusters
- Bolded values represent the best values achieved for the %NEC and %NEC S statistics comparing the PPI network and different DSD detangling thresholds