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DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism
Subcellular localization of messenger RNAs (mRNAs), as a prevalent mechanism, gives precise and efficient control for the translation process. There is mounting evidence for the important roles of this process in a variety of cellular events. Computational methods for mRNA subcellular localization p...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096227/ https://www.ncbi.nlm.nih.gov/pubmed/33503258 http://dx.doi.org/10.1093/nar/gkab016 |
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author | Wang, Duolin Zhang, Zhaoyue Jiang, Yuexu Mao, Ziting Wang, Dong Lin, Hao Xu, Dong |
author_facet | Wang, Duolin Zhang, Zhaoyue Jiang, Yuexu Mao, Ziting Wang, Dong Lin, Hao Xu, Dong |
author_sort | Wang, Duolin |
collection | PubMed |
description | Subcellular localization of messenger RNAs (mRNAs), as a prevalent mechanism, gives precise and efficient control for the translation process. There is mounting evidence for the important roles of this process in a variety of cellular events. Computational methods for mRNA subcellular localization prediction provide a useful approach for studying mRNA functions. However, few computational methods were designed for mRNA subcellular localization prediction and their performance have room for improvement. Especially, there is still no available tool to predict for mRNAs that have multiple localization annotations. In this paper, we propose a multi-head self-attention method, DM3Loc, for multi-label mRNA subcellular localization prediction. Evaluation results show that DM3Loc outperforms existing methods and tools in general. Furthermore, DM3Loc has the interpretation ability to analyze RNA-binding protein motifs and key signals on mRNAs for subcellular localization. Our analyses found hundreds of instances of mRNA isoform-specific subcellular localizations and many significantly enriched gene functions for mRNAs in different subcellular localizations. |
format | Online Article Text |
id | pubmed-8096227 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-80962272021-05-10 DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism Wang, Duolin Zhang, Zhaoyue Jiang, Yuexu Mao, Ziting Wang, Dong Lin, Hao Xu, Dong Nucleic Acids Res Methods Online Subcellular localization of messenger RNAs (mRNAs), as a prevalent mechanism, gives precise and efficient control for the translation process. There is mounting evidence for the important roles of this process in a variety of cellular events. Computational methods for mRNA subcellular localization prediction provide a useful approach for studying mRNA functions. However, few computational methods were designed for mRNA subcellular localization prediction and their performance have room for improvement. Especially, there is still no available tool to predict for mRNAs that have multiple localization annotations. In this paper, we propose a multi-head self-attention method, DM3Loc, for multi-label mRNA subcellular localization prediction. Evaluation results show that DM3Loc outperforms existing methods and tools in general. Furthermore, DM3Loc has the interpretation ability to analyze RNA-binding protein motifs and key signals on mRNAs for subcellular localization. Our analyses found hundreds of instances of mRNA isoform-specific subcellular localizations and many significantly enriched gene functions for mRNAs in different subcellular localizations. Oxford University Press 2021-01-27 /pmc/articles/PMC8096227/ /pubmed/33503258 http://dx.doi.org/10.1093/nar/gkab016 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Methods Online Wang, Duolin Zhang, Zhaoyue Jiang, Yuexu Mao, Ziting Wang, Dong Lin, Hao Xu, Dong DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism |
title | DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism |
title_full | DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism |
title_fullStr | DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism |
title_full_unstemmed | DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism |
title_short | DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism |
title_sort | dm3loc: multi-label mrna subcellular localization prediction and analysis based on multi-head self-attention mechanism |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096227/ https://www.ncbi.nlm.nih.gov/pubmed/33503258 http://dx.doi.org/10.1093/nar/gkab016 |
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