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Table 4 The performance of Modified Walktrap versus Modified Walktrap plus DSD at different edge removal thresholds; We discard clusters of size < 3, and restrict maximum cluster size to be < 100

From: RETRACTED ARTICLE: Detangling PPI networks to uncover functionally meaningful clusters

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%
  1. 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
  2. Bolded values represent the best values achieved for the %NEC and %NEC S statistics comparing the PPI network and different DSD detangling thresholds