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