An expansive PPI repository may still be beset with noise and false positives and thus, we performed a confidence assessment of the combined PPI repository and defined a reliable high quality subset termed “high-confidence direct physical PPIs (HCDP)”.
PPIs that were supported by at least two different experimental methods or two independent publications were judged to be high-confidence PPIs. High-confidence direct physical PPIs were defined as a subset of the high-confidence PPIs that satisfied at least one of the following conditions:
- Annotated as direct physical interactions in the source repositories,
- Identified by at least one qualified experimental procedure (such as yeast two-hybrid assays, fluorescence energy resonance transfer, atomic force microscopy and other methods that can detect direct physical interactions (64)),
- The supporting PMIDs.
- Chen Y-A, Tripathi LP, Mizuguchi K (2016) An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. Database (Oxford). 2016 Mar 17;2016. pii: baw009. [PubMed:26989145]