lncRNA localization and feature interpretability analysis
Subcellular localization is crucial for understanding the functions and regulatory mechanisms of biomolecules. Long non-coding RNAs (lncRNAs) have diverse roles in cellular processes, and their localization within specific subcellular compartments provides insights into their biological functions an...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | Molecular Therapy: Nucleic Acids |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253124003123 |
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| author | Jing Li Ying Ju Quan Zou Fengming Ni |
| author_facet | Jing Li Ying Ju Quan Zou Fengming Ni |
| author_sort | Jing Li |
| collection | DOAJ |
| description | Subcellular localization is crucial for understanding the functions and regulatory mechanisms of biomolecules. Long non-coding RNAs (lncRNAs) have diverse roles in cellular processes, and their localization within specific subcellular compartments provides insights into their biological functions and implications in health and disease. The nucleolus and nucleoplasm are key hubs for RNA metabolism and cellular regulation. We developed a model, LncDNN, for identifying the localization of lncRNAs in the nucleolus and nucleoplasm. LncDNN uses three different encoding schemes and employs Shapley Additive Explanations for feature analysis and selection. The results show that LncDNN is more accurate than other models. Additionally, an interpretable analysis of the features influencing the model was conducted. LncDNN is applicable for identifying the localization of lncRNA in the nucleolus and nucleoplasm, aiding in the understanding and in-depth study of related biological processes and functions. |
| format | Article |
| id | doaj-art-132ffac0be1749ee8bfdcb03fcba5416 |
| institution | Kabale University |
| issn | 2162-2531 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj-art-132ffac0be1749ee8bfdcb03fcba54162025-01-29T05:00:32ZengElsevierMolecular Therapy: Nucleic Acids2162-25312025-03-01361102425lncRNA localization and feature interpretability analysisJing Li0Ying Ju1Quan Zou2Fengming Ni3Department of Microbiology, University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, University of Hong Kong, Hong Kong, ChinaSchool of Informatics, Xiamen University, Xiamen, ChinaYangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, Zhejiang, ChinaDepartment of Gastroenterology, The First Hospital of Jilin University, Changchun, China; Corresponding author: Fengming Ni, Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China.Subcellular localization is crucial for understanding the functions and regulatory mechanisms of biomolecules. Long non-coding RNAs (lncRNAs) have diverse roles in cellular processes, and their localization within specific subcellular compartments provides insights into their biological functions and implications in health and disease. The nucleolus and nucleoplasm are key hubs for RNA metabolism and cellular regulation. We developed a model, LncDNN, for identifying the localization of lncRNAs in the nucleolus and nucleoplasm. LncDNN uses three different encoding schemes and employs Shapley Additive Explanations for feature analysis and selection. The results show that LncDNN is more accurate than other models. Additionally, an interpretable analysis of the features influencing the model was conducted. LncDNN is applicable for identifying the localization of lncRNA in the nucleolus and nucleoplasm, aiding in the understanding and in-depth study of related biological processes and functions.http://www.sciencedirect.com/science/article/pii/S2162253124003123MT: BioinformaticslncRNAssubcellular localizationnucleolusnucleoplasmmachine learning |
| spellingShingle | Jing Li Ying Ju Quan Zou Fengming Ni lncRNA localization and feature interpretability analysis Molecular Therapy: Nucleic Acids MT: Bioinformatics lncRNAs subcellular localization nucleolus nucleoplasm machine learning |
| title | lncRNA localization and feature interpretability analysis |
| title_full | lncRNA localization and feature interpretability analysis |
| title_fullStr | lncRNA localization and feature interpretability analysis |
| title_full_unstemmed | lncRNA localization and feature interpretability analysis |
| title_short | lncRNA localization and feature interpretability analysis |
| title_sort | lncrna localization and feature interpretability analysis |
| topic | MT: Bioinformatics lncRNAs subcellular localization nucleolus nucleoplasm machine learning |
| url | http://www.sciencedirect.com/science/article/pii/S2162253124003123 |
| work_keys_str_mv | AT jingli lncrnalocalizationandfeatureinterpretabilityanalysis AT yingju lncrnalocalizationandfeatureinterpretabilityanalysis AT quanzou lncrnalocalizationandfeatureinterpretabilityanalysis AT fengmingni lncrnalocalizationandfeatureinterpretabilityanalysis |