Resolution:
## Figure 1.
IDBOS scoring schemes. The method presented is an extension to the interaction detection based on shuffling
(IDBOS) method used for mass spectrometry co-purification data [22]. We compared the set of known protein-protein interactions (PPIs) with randomized
versions, which preserve the number of interactions per protein, to obtain a Z-score
and a p-value for each interaction. These quantities are schematically outlined at
the top, where a randomized probability density distribution function (PDF) is used
to illustrate the p-value and Z-score calculations for a particular interaction between
proteins i and j. To evaluate these scoring schemes, we analyzed interactions derived from crystallographic
complexes in the PDB. Each human PPI was compared to a PPI derived from protein structure
data in the PDB and assigned to one of two subsets: interactions or non-interactions. If the PPI was present in the PDB interaction data set, the pair was assigned to
the interactions set, otherwise the pair was assigned to the non-interactions set. It is reasonable to assume that the first subset should be enriched with actual
PPIs. (A) Distribution of Z-scores corresponding to “interactions” and “non-interactions”
assigned to PDB-derived PPIs, and (B) the corresponding p-value distributions. We
found that both p-values and Z-scores could distinguish these subsets, suggesting
that they are useful metrics.
Yu |