Deafness gene screening based on a multilevel cascaded BPNN model
Abstract Sudden sensorineural hearing loss is a common and frequently occurring condition in otolaryngology. Existing studies have shown that sudden sensorineural hearing loss is closely associated with mutations in genes for inherited deafness. To identify these genes associated with deafness, rese...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05182-7 |
| _version_ | 1797863308109283328 |
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| author | Xiao Liu Li Teng Wenqi Zuo Shixun Zhong Yuqiao Xu Jing Sun |
| author_facet | Xiao Liu Li Teng Wenqi Zuo Shixun Zhong Yuqiao Xu Jing Sun |
| author_sort | Xiao Liu |
| collection | DOAJ |
| description | Abstract Sudden sensorineural hearing loss is a common and frequently occurring condition in otolaryngology. Existing studies have shown that sudden sensorineural hearing loss is closely associated with mutations in genes for inherited deafness. To identify these genes associated with deafness, researchers have mostly used biological experiments, which are accurate but time-consuming and laborious. In this paper, we proposed a computational method based on machine learning to predict deafness-associated genes. The model is based on several basic backpropagation neural networks (BPNNs), which were cascaded as multiple-level BPNN models. The cascaded BPNN model showed a stronger ability for screening deafness-associated genes than the conventional BPNN. A total of 211 of 214 deafness-associated genes from the deafness variant database (DVD v9.0) were used as positive data, and 2110 genes extracted from chromosomes were used as negative data to train our model. The test achieved a mean AUC higher than 0.98. Furthermore, to illustrate the predictive performance of the model for suspected deafness-associated genes, we analyzed the remaining 17,711 genes in the human genome and screened the 20 genes with the highest scores as highly suspected deafness-associated genes. Among these 20 predicted genes, three genes were mentioned as deafness-associated genes in the literature. The analysis showed that our approach has the potential to screen out highly suspected deafness-associated genes from a large number of genes, and our predictions could be valuable for future research and discovery of deafness-associated genes. |
| first_indexed | 2024-04-09T22:34:34Z |
| format | Article |
| id | doaj.art-07e495cb7bee4f96a3cff73f647499f0 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T22:34:34Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-07e495cb7bee4f96a3cff73f647499f02023-03-22T12:33:31ZengBMCBMC Bioinformatics1471-21052023-02-0124111710.1186/s12859-023-05182-7Deafness gene screening based on a multilevel cascaded BPNN modelXiao Liu0Li Teng1Wenqi Zuo2Shixun Zhong3Yuqiao Xu4Jing Sun5School of Microelectronics and Communication Engineering, Chongqing UniversitySchool of Microelectronics and Communication Engineering, Chongqing UniversityDepartment of Otolaryngology, The First Affiliated Hospital of Chongqing Medical UniversityDepartment of Otolaryngology, The First Affiliated Hospital of Chongqing Medical UniversitySchool of Microelectronics and Communication Engineering, Chongqing UniversitySchool of Microelectronics and Communication Engineering, Chongqing UniversityAbstract Sudden sensorineural hearing loss is a common and frequently occurring condition in otolaryngology. Existing studies have shown that sudden sensorineural hearing loss is closely associated with mutations in genes for inherited deafness. To identify these genes associated with deafness, researchers have mostly used biological experiments, which are accurate but time-consuming and laborious. In this paper, we proposed a computational method based on machine learning to predict deafness-associated genes. The model is based on several basic backpropagation neural networks (BPNNs), which were cascaded as multiple-level BPNN models. The cascaded BPNN model showed a stronger ability for screening deafness-associated genes than the conventional BPNN. A total of 211 of 214 deafness-associated genes from the deafness variant database (DVD v9.0) were used as positive data, and 2110 genes extracted from chromosomes were used as negative data to train our model. The test achieved a mean AUC higher than 0.98. Furthermore, to illustrate the predictive performance of the model for suspected deafness-associated genes, we analyzed the remaining 17,711 genes in the human genome and screened the 20 genes with the highest scores as highly suspected deafness-associated genes. Among these 20 predicted genes, three genes were mentioned as deafness-associated genes in the literature. The analysis showed that our approach has the potential to screen out highly suspected deafness-associated genes from a large number of genes, and our predictions could be valuable for future research and discovery of deafness-associated genes.https://doi.org/10.1186/s12859-023-05182-7Sudden sensorineural hearing lossBackpropagation neural networkCascaded BPNN modelHighly suspected deafness-related genes |
| spellingShingle | Xiao Liu Li Teng Wenqi Zuo Shixun Zhong Yuqiao Xu Jing Sun Deafness gene screening based on a multilevel cascaded BPNN model BMC Bioinformatics Sudden sensorineural hearing loss Backpropagation neural network Cascaded BPNN model Highly suspected deafness-related genes |
| title | Deafness gene screening based on a multilevel cascaded BPNN model |
| title_full | Deafness gene screening based on a multilevel cascaded BPNN model |
| title_fullStr | Deafness gene screening based on a multilevel cascaded BPNN model |
| title_full_unstemmed | Deafness gene screening based on a multilevel cascaded BPNN model |
| title_short | Deafness gene screening based on a multilevel cascaded BPNN model |
| title_sort | deafness gene screening based on a multilevel cascaded bpnn model |
| topic | Sudden sensorineural hearing loss Backpropagation neural network Cascaded BPNN model Highly suspected deafness-related genes |
| url | https://doi.org/10.1186/s12859-023-05182-7 |
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