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Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging

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  • Armando Fernandes
  • Susana Vinga

Abstract

The article focus is the improvement of machine learning models capable of predicting protein expression levels based on their codon encoding. Support vector regression (SVR) and partial least squares (PLS) were used to create the models. SVR yields predictions that surpass those of PLS. It is shown that it is possible to improve the models predictive ability by using two more input features, codon identification number and codon count, besides the already used codon bias and minimum free energy. In addition, applying ensemble averaging to the SVR or PLS models also improves the results even further. The present work motivates the test of different ensembles and features with the aim of improving the prediction models whose correlation coefficients are still far from perfect. These results are relevant for the optimization of codon usage and enhancement of protein expression levels in synthetic biology problems.

Suggested Citation

  • Armando Fernandes & Susana Vinga, 2016. "Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-15, March.
    • Handle: RePEc:plo:pone00:0150369
    DOI: 10.1371/journal.pone.0150369
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    References listed on IDEAS

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    1. Mark Welch & Sridhar Govindarajan & Jon E Ness & Alan Villalobos & Austin Gurney & Jeremy Minshull & Claes Gustafsson, 2009. "Design Parameters to Control Synthetic Gene Expression in Escherichia coli," PLOS ONE, Public Library of Science, vol. 4(9), pages 1-10, September.
    2. Thomas F Clarke IV & Patricia L Clark, 2008. "Rare Codons Cluster," PLOS ONE, Public Library of Science, vol. 3(10), pages 1-5, October.
    3. Geman Donald & d'Avignon Christian & Naiman Daniel Q. & Winslow Raimond L., 2004. "Classifying Gene Expression Profiles from Pairwise mRNA Comparisons," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-22, August.
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