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Table 4 Number of false negatives for each method

From: Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions

  Number of false negatives of our method Number of false negatives of existing methods α:Number of "net" false negatives caused by the assumption * β:Number of true positives of existing methods Ratio (α/β)
Clustering coefficient verified with DDI (A) 683 514 102 249 41.0%
MCL verified with DDI (A) 726 554 76 209 36.4%
MCODE verified with DDI (A) 739 636 58 127 45.7%
Clustering coefficient verified with DDI (A + B) 636 514 76 249 30.5%
MCL verified with DDI (A + B) 722 554 85 209 40.7%
MCODE verified with DDI (A + B) 714 636 42 127 33.1%
Clustering coefficient verified with DDI (A + C) 590 514 51 249 20.5%
MCL verified with DDI (A + C) 707 554 78 209 37.3%
MCODE verified with DDI (A + C) 689 636 27 127 21.3%
  1. *Number of "net" false negatives indicates known protein complexes which were predicted by existing methods but were missed by our method, since our method works as a filter for existing methods. Because some known complexes were missed by our method for the lack of DDI annotations, we calculated number of net false negatives caused by our assumption, which indicates the number of the net false negatives that have DDI annotations (See text).