DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism |
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| Authors: | Duolin Wang Zhaoyue Zhang Yuexu Jiang Ziting Mao Dong Wang Hao Lin Dong Xu |
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| Institution: | Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO 65203, USA;Center for Information Biology, University of Electronic Science and Technology of China, Chengdu 610054, China;Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China |
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| Abstract: | 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. |
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