Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients

• Main Authors: Johannes Smolander, Alexey Stupnikov, Galina Glazko, Matthias Dehmer, Frank Emmert-Streib
• Format: Article
• Language: English
• Published: BMC 2019-12-01
• Series: BMC Cancer
• Subjects: Deep learning; Deep belief network; Classification; Non-coding RNA; Lung cancer and Machine learning
• Online Access: https://doi.org/10.1186/s12885-019-6338-1

Abstract Background Deciphering the meaning of the human DNA is an outstanding goal which would revolutionize medicine and our way for treating diseases. In recent years, non-coding RNAs have attracted much attention and shown to be functional in part. Yet the importance of these RNAs especially for higher biological functions remains under investigation. Methods In this paper, we analyze RNA-seq data, including non-coding and protein coding RNAs, from lung adenocarcinoma patients, a histologic subtype of non-small-cell lung cancer, with deep learning neural networks and other state-of-the-art classification methods. The purpose of our paper is three-fold. First, we compare the classification performance of different versions of deep belief networks with SVMs, decision trees and random forests. Second, we compare the classification capabilities of protein coding and non-coding RNAs. Third, we study the influence of feature selection on the classification performance. Results As a result, we find that deep belief networks perform at least competitively to other state-of-the-art classifiers. Second, data from non-coding RNAs perform better than coding RNAs across a number of different classification methods. This demonstrates the equivalence of predictive information as captured by non-coding RNAs compared to protein coding RNAs, conventionally used in computational diagnostics tasks. Third, we find that feature selection has in general a negative effect on the classification performance which means that unfiltered data with all features give the best classification results. Conclusions Our study is the first to use ncRNAs beyond miRNAs for the computational classification of cancer and for performing a direct comparison of the classification capabilities of protein coding RNAs and non-coding RNAs.