Zhen Cao1, Xiaoyong Pan2, Yang Yang3, Yan Huang4, Hong-Bin Shen1. 1. Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China. 2. Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands. 3. Department of Computer Science, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, China. 4. State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China.
Abstract
Motivation: The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date. Results: In this study, we report an ensemble classifier-based predictor, lncLocator, for predicting the lncRNA subcellular localizations. To fully exploit lncRNA sequence information, we adopt both k-mer features and high-level abstraction features generated by unsupervised deep models, and construct four classifiers by feeding these two types of features to support vector machine (SVM) and random forest (RF), respectively. Then we use a stacked ensemble strategy to combine the four classifiers and get the final prediction results. The current lncLocator can predict five subcellular localizations of lncRNAs, including cytoplasm, nucleus, cytosol, ribosome and exosome, and yield an overall accuracy of 0.59 on the constructed benchmark dataset. Availability and implementation: The lncLocator is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date. Results: In this study, we report an ensemble classifier-based predictor, lncLocator, for predicting the lncRNA subcellular localizations. To fully exploit lncRNA sequence information, we adopt both k-mer features and high-level abstraction features generated by unsupervised deep models, and construct four classifiers by feeding these two types of features to support vector machine (SVM) and random forest (RF), respectively. Then we use a stacked ensemble strategy to combine the four classifiers and get the final prediction results. The current lncLocator can predict five subcellular localizations of lncRNAs, including cytoplasm, nucleus, cytosol, ribosome and exosome, and yield an overall accuracy of 0.59 on the constructed benchmark dataset. Availability and implementation: The lncLocator is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator. Supplementary information: Supplementary data are available at Bioinformatics online.
Authors: Lee Jin Lim; Lay Hiang Ling; Yu Pei Neo; Alexander Y F Chung; Brian K P Goh; Pierce K H Chow; Chung Yip Chan; Peng Chung Cheow; Ser Yee Lee; Tony K H Lim; Samuel S Chong; London L P J Ooi; Caroline G Lee Journal: J Cancer Date: 2021-03-30 Impact factor: 4.207