|Evaluation of different ranking schemes|
|Reference set||IDBOS||Hypergeometric||Occurrence||Random rank|
|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