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Table 5 Evaluation of ranked interactions to detect biological relationships

From: Inferring high-confidence human protein-protein interactions

Reference set

IDBOS

Hypergeometric

Occurrence

Random rank

 

Fraction

Gain

Fraction

Gain

Fraction

Gain

Fraction

Co-pathway

0.350

76%

0.315

59%

0.235

18%

0.199

Co-disease

0.306

91%

0.298

86%

0.214

34%

0.160

Co-function

0.122

48%

0.123

50%

0.095

16%

0.082

Co-expression

0.036

15%

0.035

14%

0.033

6%

0.031

  1. The fraction of biological associations retrieved using interaction detection based on shuffling (IDBOS), hypergeometric test ranking, occurrence ranking schemes, and randomly ranked data. We calculated the reported fraction and gain associated with the different ranking schemes as outlined in Equations 3 and 4. The four reference sets tested contain putative biological relationships pertaining to protein interactions that are in the same Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway (co-pathway), implicated in the same disease (co-disease), share Gene Ontology (GO) function (co-function), or tissue expression levels (co-expression). We tested whether the numerical differences in the fraction values for each pairwise comparison within each references set were due to chance using the t-test, and rejected this hypothesis with a p-value of <10-2.