A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity
BIOTECHNOLOGY HPC SOFTWARE APPLICATIONS INST FORT DETRICK MD
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Large-scale protein interaction networks PINs have typically been discerned using affinity purification followed by mass spectrometry APMS and yeast two-hybrid Y2H techniques. It is generally recognized that Y2H screens detect direct binary interactions while the APMS method captures co-complex associations however, the latter technique is known to compute the propensity for two proteins to co-purify in an APMS data set, thereby allowing us to assess the detected level of interaction specificity by analyzing the corresponding distribution of interaction scores. We find that two recent APMS data sets of yeast contain enrichments of specific, or high-scoring, associations as compared to commensurate random profiles, and that curated, direct physical interactions in two prominent data bases have consistently high scores. Our scored interaction data sets are generally more comprehensive than those of previous studies when compared against four diverse high-quality reference sets. Furthermore, we find that our scored data sets are more enriched with curated, direct physical associations than Y2H sets.
- Industrial Chemistry and Chemical Processing
- Numerical Mathematics