Prediction of disease-related miRNAs by voting with multiple classifiers
Abstract There is strong evidence to support that mutations and dysregulation of miRNAs are associated with a variety of diseases, including cancer. However, the experimental methods used to identify disease-related miRNAs are expensive and time-consuming. Effective computational approaches to ident...
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05308-x |
| _version_ | 1797831887045001216 |
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| author | Changlong Gu Xiaoying Li |
| author_facet | Changlong Gu Xiaoying Li |
| author_sort | Changlong Gu |
| collection | DOAJ |
| description | Abstract There is strong evidence to support that mutations and dysregulation of miRNAs are associated with a variety of diseases, including cancer. However, the experimental methods used to identify disease-related miRNAs are expensive and time-consuming. Effective computational approaches to identify disease-related miRNAs are in high demand and would aid in the detection of lncRNA biomarkers for disease diagnosis, treatment, and prevention. In this study, we develop an ensemble learning framework to reveal the potential associations between miRNAs and diseases (ELMDA). The ELMDA framework does not rely on the known associations when calculating miRNA and disease similarities and uses multi-classifiers voting to predict disease-related miRNAs. As a result, the average AUC of the ELMDA framework was 0.9229 for the HMDD v2.0 database in a fivefold cross-validation. All potential associations in the HMDD V2.0 database were predicted, and 90% of the top 50 results were verified with the updated HMDD V3.2 database. The ELMDA framework was implemented to investigate gastric neoplasms, prostate neoplasms and colon neoplasms, and 100%, 94%, and 90%, respectively, of the top 50 potential miRNAs were validated by the HMDD V3.2 database. Moreover, the ELMDA framework can predict isolated disease-related miRNAs. In conclusion, ELMDA appears to be a reliable method to uncover disease-associated miRNAs. |
| first_indexed | 2024-04-09T13:58:53Z |
| format | Article |
| id | doaj.art-68b2aad1bbb44c04813b48cb0748dee6 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T13:58:53Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-68b2aad1bbb44c04813b48cb0748dee62023-05-07T11:25:50ZengBMCBMC Bioinformatics1471-21052023-04-0124111710.1186/s12859-023-05308-xPrediction of disease-related miRNAs by voting with multiple classifiersChanglong Gu0Xiaoying Li1College of Information Science and Engineering, Hunan UniversityCollege of Information Science and Engineering, Hunan UniversityAbstract There is strong evidence to support that mutations and dysregulation of miRNAs are associated with a variety of diseases, including cancer. However, the experimental methods used to identify disease-related miRNAs are expensive and time-consuming. Effective computational approaches to identify disease-related miRNAs are in high demand and would aid in the detection of lncRNA biomarkers for disease diagnosis, treatment, and prevention. In this study, we develop an ensemble learning framework to reveal the potential associations between miRNAs and diseases (ELMDA). The ELMDA framework does not rely on the known associations when calculating miRNA and disease similarities and uses multi-classifiers voting to predict disease-related miRNAs. As a result, the average AUC of the ELMDA framework was 0.9229 for the HMDD v2.0 database in a fivefold cross-validation. All potential associations in the HMDD V2.0 database were predicted, and 90% of the top 50 results were verified with the updated HMDD V3.2 database. The ELMDA framework was implemented to investigate gastric neoplasms, prostate neoplasms and colon neoplasms, and 100%, 94%, and 90%, respectively, of the top 50 potential miRNAs were validated by the HMDD V3.2 database. Moreover, the ELMDA framework can predict isolated disease-related miRNAs. In conclusion, ELMDA appears to be a reliable method to uncover disease-associated miRNAs.https://doi.org/10.1186/s12859-023-05308-xmiRNA similarityDisease similarityMulti-classifiers votingCross-validationXGBoost classificationRandom forest classification |
| spellingShingle | Changlong Gu Xiaoying Li Prediction of disease-related miRNAs by voting with multiple classifiers BMC Bioinformatics miRNA similarity Disease similarity Multi-classifiers voting Cross-validation XGBoost classification Random forest classification |
| title | Prediction of disease-related miRNAs by voting with multiple classifiers |
| title_full | Prediction of disease-related miRNAs by voting with multiple classifiers |
| title_fullStr | Prediction of disease-related miRNAs by voting with multiple classifiers |
| title_full_unstemmed | Prediction of disease-related miRNAs by voting with multiple classifiers |
| title_short | Prediction of disease-related miRNAs by voting with multiple classifiers |
| title_sort | prediction of disease related mirnas by voting with multiple classifiers |
| topic | miRNA similarity Disease similarity Multi-classifiers voting Cross-validation XGBoost classification Random forest classification |
| url | https://doi.org/10.1186/s12859-023-05308-x |
| work_keys_str_mv | AT changlonggu predictionofdiseaserelatedmirnasbyvotingwithmultipleclassifiers AT xiaoyingli predictionofdiseaserelatedmirnasbyvotingwithmultipleclassifiers |