Comparing Methods for Assigning Confidence to Protein Interactions
Author Information
Author(s): Suthram Silpa, Shlomi Tomer, Ruppin Eytan, Sharan Roded, Ideker Trey
Primary Institution: University of California, San Diego
Hypothesis
How do different confidence assignment schemes for protein interactions compare in terms of performance?
Conclusion
Deng et al. yields the best performance overall among the confidence assignment schemes evaluated.
Supporting Evidence
- Deng et al. performed best in three out of four metrics.
- Bader et al. and Sharan methods performed similarly across most metrics.
- Using any probability assignment scheme is better than assuming all interactions are equally likely.
Takeaway
The study looks at different ways to measure how likely it is that proteins interact with each other, finding that some methods work better than others.
Methodology
The study compares seven different confidence assignment schemes using a test set of 11,883 yeast interactions and evaluates their performance based on various biological attributes.
Potential Biases
Potential bias may arise from the reliance on previously established gold standards for training the confidence assignment schemes.
Limitations
The study's findings may be limited by the specific datasets and methods used for comparison.
Participant Demographics
The study focuses on protein interactions in Saccharomyces cerevisiae (yeast).
Statistical Information
P-Value
p<0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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