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Amino Acids

, Volume 48, Issue 7, pp 1655–1665 | Cite as

SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information

  • Xuhan Liu
  • Shiping Yang
  • Chen Li
  • Ziding ZhangEmail author
  • Jiangning SongEmail author
Original Article

Abstract

Protein self-interaction, i.e. the interaction between two or more identical proteins expressed by one gene, plays an important role in the regulation of cellular functions. Considering the limitations of experimental self-interaction identification, it is necessary to design specific bioinformatics tools for self-interacting protein (SIP) prediction from protein sequence information. In this study, we proposed an improved computational approach for SIP prediction, termed SPAR (Self-interacting Protein Analysis serveR). Firstly, we developed an improved encoding scheme named critical residues substitution (CRS), in which the fine-grained domain–domain interaction information was taken into account. Then, by employing the Random Forest algorithm, the performance of CRS was evaluated and compared with several other encoding schemes commonly used for sequence-based protein–protein interaction prediction. Through the tenfold cross-validation tests on a balanced training dataset, CRS performed the best, with the average accuracy up to 72.01 %. We further integrated CRS with other encoding schemes and identified the most important features using the mRMR (the minimum redundancy maximum relevance) feature selection method. Our SPAR model with selected features achieved an average accuracy of 92.09 % on the human-independent test set (the ratio of positives to negatives was about 1:11). Besides, we also evaluated the performance of SPAR on an independent yeast test set (the ratio of positives to negatives was about 1:8) and obtained an average accuracy of 76.96 %. The results demonstrate that SPAR is capable of achieving a reasonable performance in cross-species application. The SPAR server is freely available for academic use at http://systbio.cau.edu.cn/zzdlab/spar/.

Keywords

Self-interacting protein Prediction Machine learning Feature selection Domain–domain interaction 

Notes

Acknowledgments

We thank Dr. Yuan Zhou at China Agricultural University for helpful discussions on this work. This work was supported by grants from the National Natural Science Foundation of China (31271414, 31471249, 61202167, 61303169).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

726_2016_2226_MOESM1_ESM.docx (24 kb)
Supplementary material 1 (DOCX 23 kb)

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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  1. 1.State Key Laboratory of Agrobiotechnology, College of Biological SciencesChina Agricultural UniversityBeijingChina
  2. 2.Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityMelbourneAustralia
  3. 3.Monash Centre for Data Science, Faculty of Information TechnologyMonash UniversityMelbourneAustralia
  4. 4.National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina

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