Mammalian piRNA target prediction using a hierarchical attention model
Abstract Background Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important roles in regulating mRNA transcript levels. Despite their significant role...
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| Language: | English |
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BMC
2025-02-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06068-6 |
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| author | Tianjiao Zhang Liang Chen Haibin Zhu Garry Wong |
| author_facet | Tianjiao Zhang Liang Chen Haibin Zhu Garry Wong |
| author_sort | Tianjiao Zhang |
| collection | DOAJ |
| description | Abstract Background Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important roles in regulating mRNA transcript levels. Despite their significant role in regulating cellular RNA levels, the piRNA targeting rules are not well defined, especially in mammals, which poses obstacles to the elucidation of piRNA function. Results Given the complexity and current limitation in understanding the mammalian piRNA targeting rules, we designed a deep learning model by selecting appropriate deep learning sub-networks based on the targeting patterns of piRNA inferred from previous experiments. Additionally, to alleviate the problem of insufficient data, a transfer learning approach was employed. Our model achieves a good discriminatory power (Accuracy: 98.5%) in predicting an independent test dataset. Finally, this model was utilized to predict the targets of all mouse and human piRNAs available in the piRNA database. Conclusions In this research, we developed a deep learning framework that significantly advances the prediction of piRNA targets, overcoming the limitations posed by insufficient data and current incomplete targeting rules. The piRNA target prediction network and results can be downloaded from https://github.com/SofiaTianjiaoZhang/piRNATarget . |
| format | Article |
| id | doaj-art-b1fc67f3268f44538cde481ceda81bd0 |
| institution | DOAJ |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-b1fc67f3268f44538cde481ceda81bd02025-08-20T02:43:13ZengBMCBMC Bioinformatics1471-21052025-02-0126111710.1186/s12859-025-06068-6Mammalian piRNA target prediction using a hierarchical attention modelTianjiao Zhang0Liang Chen1Haibin Zhu2Garry Wong3School of Pharmacy and Food Engineering, Wuyi UniversityDepartment of Computer Science and Technology, College of Mathematics and Computer, Shantou UniversityDepartment of Statistics and Data Science, School of Economics, Jinan UniversityFaculty of Health Sciences, University of MacauAbstract Background Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important roles in regulating mRNA transcript levels. Despite their significant role in regulating cellular RNA levels, the piRNA targeting rules are not well defined, especially in mammals, which poses obstacles to the elucidation of piRNA function. Results Given the complexity and current limitation in understanding the mammalian piRNA targeting rules, we designed a deep learning model by selecting appropriate deep learning sub-networks based on the targeting patterns of piRNA inferred from previous experiments. Additionally, to alleviate the problem of insufficient data, a transfer learning approach was employed. Our model achieves a good discriminatory power (Accuracy: 98.5%) in predicting an independent test dataset. Finally, this model was utilized to predict the targets of all mouse and human piRNAs available in the piRNA database. Conclusions In this research, we developed a deep learning framework that significantly advances the prediction of piRNA targets, overcoming the limitations posed by insufficient data and current incomplete targeting rules. The piRNA target prediction network and results can be downloaded from https://github.com/SofiaTianjiaoZhang/piRNATarget .https://doi.org/10.1186/s12859-025-06068-6piRNADeep learningTransfer learning |
| spellingShingle | Tianjiao Zhang Liang Chen Haibin Zhu Garry Wong Mammalian piRNA target prediction using a hierarchical attention model BMC Bioinformatics piRNA Deep learning Transfer learning |
| title | Mammalian piRNA target prediction using a hierarchical attention model |
| title_full | Mammalian piRNA target prediction using a hierarchical attention model |
| title_fullStr | Mammalian piRNA target prediction using a hierarchical attention model |
| title_full_unstemmed | Mammalian piRNA target prediction using a hierarchical attention model |
| title_short | Mammalian piRNA target prediction using a hierarchical attention model |
| title_sort | mammalian pirna target prediction using a hierarchical attention model |
| topic | piRNA Deep learning Transfer learning |
| url | https://doi.org/10.1186/s12859-025-06068-6 |
| work_keys_str_mv | AT tianjiaozhang mammalianpirnatargetpredictionusingahierarchicalattentionmodel AT liangchen mammalianpirnatargetpredictionusingahierarchicalattentionmodel AT haibinzhu mammalianpirnatargetpredictionusingahierarchicalattentionmodel AT garrywong mammalianpirnatargetpredictionusingahierarchicalattentionmodel |