Table 3

Evaluation of different ranking schemes
Reference set IDBOS Hypergeometric Occurrence Random rank
<A> Gain <A> Gain <A> Gain <A>
Far-Western blotting 0.409 184% 0.313 118% 0.178 24% 0.144
Isothermal titration calorimetry 0.542 215% 0.469 173% 0.286 66% 0.172
Nuclear magnetic resonance 0.632 157% 0.534 117% 0.331 34% 0.246
Surface plasmon resonance 0.567 160% 0.496 128% 0.320 47% 0.218
PDB complex PPIs 0.842 258% 0.746 217% 0.566 141% 0.235
Mouse homologous PPIs 0.318 222% 0.293 198% 0.207 110% 0.099

The average accuracy < A > and gain associated with interaction detection based on shuffling (IDBOS), hypergeometric test ranking, and occurrence-ranking schemes were estimated using Equations 3 and 4. The value associated with the randomly ranked data set does not represent a random protein-protein interaction (PPI) data set as only the rank, and not the interactions themselves, were randomized. The tested reference sets contain PPIs derived from 1) far-Western blotting, 2) isothermal titration calorimetry, 3) nuclear magnetic resonance, 4) surface plasmon resonance experiments, 5) known protein crystal complexes contained in the Protein Data Bank (PDB), and 6) those derived from experimentally determined mouse PPIs. We tested whether the numerical differences in values of < A > for each pairwise comparison within each reference set were due to chance using the t-test, and rejected this hypothesis with a p-value of <10-6.

Yu et al.

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

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