Table 5

Evaluation of ranked interactions to detect biological relationships
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

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.

Yu et al.

Yu et al. BMC Bioinformatics 2012 13:79   doi:10.1186/1471-2105-13-79

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