DeepUEP: Prediction of Urine Excretory Proteins Using Deep Learning

Abstract

Urine excretory proteins are among the most commonly used biomarkers in body fluids. Computational identification of urine excretory proteins can provide very useful information for identifying targeted disease biomarkers in urine by linking transcriptome or proteomics data. There are few methods based on conventional machine learning algorithms for predicting urine excretory proteins, and most of these methods strongly depend on the extraction of features from urine excretory proteins. An end-to-end model for urine excretory protein prediction, called DeepUEP, is presented using deep neural networks relying on only amino acid sequence information. The model achieves good performance and outperforms existing methods on training and testing sets. By comparing known urinary protein biomarkers with the results of the model, we find that the model can achieve a true-positive rate of over 80% for urinary protein biomarkers that have been detected in more than one study. We also combine our model with transcriptome and proteomics data from lung cancer patients to predict the potential urinary protein biomarkers of lung cancer. A web server is developed for the prediction of urine excretory proteins, and it can be accessed at the following URL: <uri xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.csbg-jlu.info/DeepUEP/</uri> . We believe that our prediction model and web server are useful for biomedical researchers who are interested in identifying urinary protein biomarkers, especially for candidate proteins in transcriptome or proteomics analyses of diseased tissues.