Computational prediction of disease related lncRNAs using machine learning
Razia Khalid, Hammad Naveed, Zoya Khalid
Abstract
Long non-coding RNAs (lncRNAs), which were once considered as transcriptional noise, are now in the limelight of current research. LncRNAs play a major role in regulating various biological processes such as imprinting, cell differentiation, and splicing. The mutations of lncRNAs are involved in various complex diseases. Identifying lncRNA-disease associations has gained a lot of attention as predicting it efficiently will lead towards better disease treatment. In this study, we have developed a machine learning model that predicts disease-related lncRNAs by combining sequence and structure-based features. The features were trained on SVM and Random Forest classifiers. We have compared our method with the state-of-the-art and obtained the highest F1 score of 76% on SVM classifier. Moreover, this study has overcome two serious limitations of the reported method which are lack of redundancy checking and implementation of oversampling for balancing the positive and negative class. Our method has achieved improved performance among machine learning models reported for lncRNA-disease associations. Combining multiple features together specifically lncRNAs sequence mutation has a significant contribution to the disease related lncRNA prediction.