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PLoS One. 2011 Mar 10;6(3):e17668. doi: 10.1371/journal.pone.0017668.

Predicting protein phenotypes based on protein-protein interaction network.

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  • 1Institute of Systems Biology, Shanghai University, Shanghai, China.



Identifying associated phenotypes of proteins is a challenge of the modern genetics since the multifactorial trait often results from contributions of many proteins. Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins.


Here, we proposed a new method for predicting protein phenotypes in yeast based on protein-protein interaction network. Instead of only the most likely phenotype, a series of possible phenotypes for the query protein were generated and ranked according to the tethering potential score. As a result, the first order prediction accuracy of our method achieved 65.4% evaluated by Jackknife test of 1,267 proteins in budding yeast, much higher than the success rate (15.4%) of a random guess. And the likelihood of the first 3 predicted phenotypes including all the real phenotypes of the proteins was 70.6%.


The candidate phenotypes predicted by our method provided useful clues for the further validation. In addition, the method can be easily applied to the prediction of protein associated phenotypes in other organisms.

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