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Table 2 Evaluation of true prediction performance on Dset2

From: Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators

Method  TP  FP  TN  FN  Sp (%)  Re (%)  Pr (%)  F
PSOPIA (θ = 0.293, the higheset F)  143  5,026  1,766,423  4,152  99.72  3.33  2.77  0.030
PSOPIA (θ = 0.670)  24  151  1,771,298  4,271  99.99  0.56  13.71  0.012
PSOPIA (θ = 0.890)  4  31  1,771,418  4,291  99.99  0.09  11.43  0.002
(I) BIPS, only filtered by the template interactions
(A) Template: Taxonomy ID = 9609 (human)  19  680  1,765,404  3,710  99.96  0.51  2.72  0.009
(B) Template: all species  19  833  1,765,005  3,705  99.95  0.51  2.23  0.008
(II) BIPS, filtered by known DDIs (iPfam or 3DID)
(A) Template: Taxonomy ID = 9609 (human)  5  60  1,771,096  4,261  99.99  0.12  7,69  0.002
(B) Template: all species  5  72  1,771,059  4,256  99.99  0.12  6.49  0.002
(III) BIPS, filtered by known DDIs (iPfam or 3DID) and GO; biological process, cellular component or molecular function
(A) Template: Taxonomy ID = 9609 (human)  3  47  1,771,245  4,284  99.99  0.07  6.00  0.001
(B) Template: all species  3 56  1,771,216  4,280  99.99  0.07  5.08  0.001
  1. For PSOPIA trained on Dset1 (a data set independent of Dset2), the best threshold value, 0.995, which gave the highest F-measure in the 10-fold CV, was used to classify a pair of proteins as interacting or non-interacting. For BIPS, the default values in homologue conditions were used: joint identities ≥ 80%, joint e-values ≥ 1.0 × e−10, and template sequence coverage ≥ 80% (see [21] for more details of these parameters). In addition to the filtering by the template interactions only (I), two additional filters were applied: (II) filtered by known DDIs in iPfam or 3DID and (III) filtered by known DDIs and GO annotations (biological process, cellular component or molecular function). Furthermore, two template interactions, (A) only from human (taxonomy ID = 9609) and (B) from all species, were also considered.