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lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning

Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and human complex diseases. Distinguishing lncRNAs from protein-coding transcripts is a fundamental step for analyzing the lncRNA functional mechanism. However, the experimental identification of lncRNAs is expensive a...

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Detalles Bibliográficos
Autores principales: Fan, Xiao-Nan, Zhang, Shao-Wu, Zhang, Song-Yao, Ni, Jin-Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7432689/
https://www.ncbi.nlm.nih.gov/pubmed/32718000
http://dx.doi.org/10.3390/ijms21155222
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author Fan, Xiao-Nan
Zhang, Shao-Wu
Zhang, Song-Yao
Ni, Jin-Jie
author_facet Fan, Xiao-Nan
Zhang, Shao-Wu
Zhang, Song-Yao
Ni, Jin-Jie
author_sort Fan, Xiao-Nan
collection PubMed
description Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and human complex diseases. Distinguishing lncRNAs from protein-coding transcripts is a fundamental step for analyzing the lncRNA functional mechanism. However, the experimental identification of lncRNAs is expensive and time-consuming. In this study, we presented an alignment-free multimodal deep learning framework (namely lncRNA_Mdeep) to distinguish lncRNAs from protein-coding transcripts. LncRNA_Mdeep incorporated three different input modalities, then a multimodal deep learning framework was built for learning the high-level abstract representations and predicting the probability whether a transcript was lncRNA or not. LncRNA_Mdeep achieved 98.73% prediction accuracy in a 10-fold cross-validation test on humans. Compared with other eight state-of-the-art methods, lncRNA_Mdeep showed 93.12% prediction accuracy independent test on humans, which was 0.94%~15.41% higher than that of other eight methods. In addition, the results on 11 cross-species datasets showed that lncRNA_Mdeep was a powerful predictor for predicting lncRNAs.
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spelling pubmed-74326892020-08-27 lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning Fan, Xiao-Nan Zhang, Shao-Wu Zhang, Song-Yao Ni, Jin-Jie Int J Mol Sci Article Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and human complex diseases. Distinguishing lncRNAs from protein-coding transcripts is a fundamental step for analyzing the lncRNA functional mechanism. However, the experimental identification of lncRNAs is expensive and time-consuming. In this study, we presented an alignment-free multimodal deep learning framework (namely lncRNA_Mdeep) to distinguish lncRNAs from protein-coding transcripts. LncRNA_Mdeep incorporated three different input modalities, then a multimodal deep learning framework was built for learning the high-level abstract representations and predicting the probability whether a transcript was lncRNA or not. LncRNA_Mdeep achieved 98.73% prediction accuracy in a 10-fold cross-validation test on humans. Compared with other eight state-of-the-art methods, lncRNA_Mdeep showed 93.12% prediction accuracy independent test on humans, which was 0.94%~15.41% higher than that of other eight methods. In addition, the results on 11 cross-species datasets showed that lncRNA_Mdeep was a powerful predictor for predicting lncRNAs. MDPI 2020-07-23 /pmc/articles/PMC7432689/ /pubmed/32718000 http://dx.doi.org/10.3390/ijms21155222 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Fan, Xiao-Nan
Zhang, Shao-Wu
Zhang, Song-Yao
Ni, Jin-Jie
lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning
title lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning
title_full lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning
title_fullStr lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning
title_full_unstemmed lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning
title_short lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning
title_sort lncrna_mdeep: an alignment-free predictor for distinguishing long non-coding rnas from protein-coding transcripts by multimodal deep learning
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7432689/
https://www.ncbi.nlm.nih.gov/pubmed/32718000
http://dx.doi.org/10.3390/ijms21155222
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