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Title: PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction

Determining protein-protein interaction (PPI) in biological systems is of considerable importance, and prediction of PPI has become a popular research area. Although different classifiers have been developed for PPI prediction, no single classifier seems to be able to predict PPI with high confidence. We postulated that by combining individual classifiers the accuracy of PPI prediction could be improved. We developed a method called protein-protein interaction prediction classifiers merger (PPCM), and this method combines output from two PPI prediction tools, GO2PPI and Phyloprof, using Random Forests algorithm. The performance of PPCM was tested by area under the curve (AUC) using an assembled Gold Standard database that contains both positive and negative PPI pairs. Our AUC test showed that PPCM significantly improved the PPI prediction accuracy over the corresponding individual classifiers. We found that additional classifiers incorporated into PPCM could lead to further improvement in the PPI prediction accuracy. Furthermore, cross species PPCM could achieve competitive and even better prediction accuracy compared to the single species PPCM. This study established a robust pipeline for PPI prediction by integrating multiple classifiers using Random Forests algorithm. This pipeline will be useful for predicting PPI in nonmodel species.
Authors:
 [1] ;  [1] ;  [2]
  1. Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
  2. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Publication Date:
OSTI Identifier:
1234001
Grant/Contract Number:
DE–AC05–00OR22725
Type:
Published Article
Journal Name:
International Journal of Genomics
Additional Journal Information:
Journal Volume: 2015; Related Information: CHORUS Timestamp: 2016-07-27 18:35:42; Journal ID: ISSN 2314-436X
Publisher:
Hindawi Publishing Corporation
Sponsoring Org:
USDOE
Country of Publication:
Egypt
Language:
English