Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification

Bioinformatics
Jingpu ZhangLei Deng

Abstract

Long non-coding RNAs (lncRNAs) are an enormous collection of functional non-coding RNAs. Over the past decades, a large number of novel lncRNA genes have been identified. However, most of the lncRNAs remain function uncharacterized at present. Computational approaches provide a new insight to understand the potential functional implications of lncRNAs. Considering that each lncRNA may have multiple functions and a function may be further specialized into sub-functions, here we describe NeuraNetL2GO, a computational ontological function prediction approach for lncRNAs using hierarchical multi-label classification strategy based on multiple neural networks. The neural networks are incrementally trained level by level, each performing the prediction of gene ontology (GO) terms belonging to a given level. In NeuraNetL2GO, we use topological features of the lncRNA similarity network as the input of the neural networks and employ the output results to annotate the lncRNAs. We show that NeuraNetL2GO achieves the best performance and the overall advantage in maximum F-measure and coverage on the manually annotated lncRNA2GO-55 dataset compared to other state-of-the-art methods. The source code and data are available at http://denglab.o...Continue Reading

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Citations

Jul 18, 2018·International Journal of Molecular Sciences·Mengting NiuKe Han
Aug 7, 2018·Expert Opinion on Drug Discovery·Ilya BlokhinClaes Wahlestedt
Dec 21, 2019·BMC Medical Informatics and Decision Making·Lei DengJingpu Zhang
Nov 21, 2018·BMC Medical Genomics·Jingpu ZhangLei Deng
Feb 15, 2019·Frontiers in Genetics·Lei DengJingpu Zhang
May 26, 2018·Nature Reviews. Genetics·Barbara Uszczynska-RatajczakRory Johnson
Dec 21, 2018·BMC Bioinformatics·Rezvan Ehsani, Finn Drabløs
Mar 3, 2020·Frontiers in Genetics·Chunyu WangMaozu Guo
Jul 3, 2018·Database : the Journal of Biological Databases and Curation·Cheng ZengLei Deng
Jan 18, 2020·Current Pharmaceutical Design·Jiajie PengXuequn Shang
Jun 14, 2020·Current Pharmaceutical Design·Shuai DengTianyi Zang
May 2, 2021·BMC Research Notes·Casper van MourikFinn Drabløs
Jan 31, 2019·Journal of Proteome Research·Yanjuan LiQuan Zou

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