Deep-RBPPred: Predicting RNA Binding Proteins in the Proteome Scale Based on Deep Learning

Sci Rep. 2018 Oct 15;8(1):15264. doi: 10.1038/s41598-018-33654-x.

Abstract

RNA binding protein (RBP) plays an important role in cellular processes. Identifying RBPs by computation and experiment are both essential. Recently, an RBP predictor, RBPPred, is proposed in our group to predict RBPs. However, RBPPred is too slow for that it needs to generate PSSM matrix as its feature. Herein, based on the protein feature of RBPPred and Convolutional Neural Network (CNN), we develop a deep learning model called Deep-RBPPred. With the balance and imbalance training set, we obtain Deep-RBPPred-balance and Deep-RBPPred-imbalance models. Deep-RBPPred has three advantages comparing to previous methods. (1) Deep-RBPPred only needs few physicochemical properties based on protein sequences. (2) Deep-RBPPred runs much faster. (3) Deep-RBPPred has a good generalization ability. In the meantime, Deep-RBPPred is still as good as the state-of-the-art method. Testing in A. thaliana, S. cerevisiae and H. sapiens proteomes, MCC values are 0.82 (0.82), 0.65 (0.69) and 0.85 (0.80) for balance model (imbalance model) when the score cutoff is set to 0.5, respectively. In the same testing dataset, different machine learning algorithms (CNN and SVM) are also compared. The results show that CNN-based model can identify more RBPs than SVM-based. In comparing the balance and imbalance model, both CNN-base and SVM-based tend to favor the majority class in the imbalance set. Deep-RBPPred forecasts 280 (balance model) and 265 (imbalance model) of 299 new RBP. The sensitivity of balance model is about 7% higher than the state-of-the-art method. We also apply deep-RBPPred to 30 eukaryotes and 109 bacteria proteomes downloaded from Uniprot to estimate all possible RBPs. The estimating result shows that rates of RBPs in eukaryote proteomes are much higher than bacteria proteomes.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Computational Biology / methods*
  • Databases, Protein
  • Deep Learning*
  • Machine Learning
  • Neural Networks, Computer
  • Proteome
  • RNA-Binding Proteins / analysis*
  • RNA-Binding Proteins / isolation & purification
  • RNA-Binding Proteins / metabolism
  • Sensitivity and Specificity
  • Sequence Analysis, Protein / methods*

Substances

  • Proteome
  • RNA-Binding Proteins