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Table 1 Maximum F-measure (\(F_{max}\)) scores obtained with DomFun using the CAFA 3 prediction benchmark

From: Assigning protein function from domain-function associations using DomFun

Domain classification

FA

Association + combination methods

HyI + Fis

PCC+Sto

Jac + Sto

Sim+Sto

\(F_{max}\) values from PR curves (domain-FunFys associations for CAFA 3 target proteins)

 FunFams

GOMF

0.608

0.553

0.515

0.624

GOBP

0.452

0.444

0.443

0.492

GOCC

0.542

0.529

0.529

0.602

 Superfamilies

GOMF

0.314

0.347

0.350

0.384

GOBP

0.099

0.172

0.238

0.174

GOCC

0.254

0.353

0.398

0.340

  1. The best performing methods for each domain/GO subontology combination are indicated in bold
  2. FA Functional annotation, HyI hypergeometric index, Sim Simpson index, PCC Pearson correlation coefficient, Jac Jaccard index, Sto Stouffer’s combination method, Fis Fisher’s combined probability test. CAFA 3 evaluation procedure set to partial mode and limited knowledge