Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease Associations
Identifying disease-associated miRNAs is helpful to explore the pathogenesis of diseases. However, without foreknowledge of the experimentally valid disease-associated miRNAs information, the development of promising and affordable approaches for effective treatment of human diseases is challenging....
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doaj-cc99179d5ab9404593f9adeef546ad0a2021-03-30T04:39:14ZengIEEEIEEE Access2169-35362020-01-01813317013317910.1109/ACCESS.2020.30069989133264Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease AssociationsYajie Meng0https://orcid.org/0000-0002-2384-1158Min Jin1https://orcid.org/0000-0002-4858-8048Xianfang Tang2Junlin Xu3https://orcid.org/0000-0003-1057-1504College of Computer Science and Electronic Engineering, Hunan University, Changsha, ChinaCollege of Computer Science and Electronic Engineering, Hunan University, Changsha, ChinaCollege of Computer Science and Electronic Engineering, Hunan University, Changsha, ChinaCollege of Computer Science and Electronic Engineering, Hunan University, Changsha, ChinaIdentifying disease-associated miRNAs is helpful to explore the pathogenesis of diseases. However, without foreknowledge of the experimentally valid disease-associated miRNAs information, the development of promising and affordable approaches for effective treatment of human diseases is challenging. In this study, we develop DCNMDA and DJMDA, a degree-based similarity indexes methodology for identifying potential miRNAs-disease associations. We solely focused on the similarity and the degree between nodes without adopting negative samples or other external prior information beyond the miRNA-disease associations bipartite network. Trained on HMDD v2.0 and HMDD v3.0, DCNMDA achieved the highest AUCs (0.9237 and 0.9432, respectively) based on the 5-fold cross-validation and outperformed the published state-of-the-art methodologies. Moreover, case studies about breast neoplasms, lung neoplasms, and ovarian neoplasms further evaluate the reliability of the models. As a result, biological experiments can correspondingly verify 28 out of top-30 DJMDA-predicted MDAs and 29 out of top-30 DCNMDA-predicted MDAs. In summary, DCNMDA and DJMDA offer a powerful degree-based similarity index approach for identifying potential miRNAs-disease associations with superior performance.https://ieeexplore.ieee.org/document/9133264/miRNA-disease associationsdegree-based similarity indexescommon neighbor and Jaccardarea under curve (AUC)area under the precise recall curve (AUPR) |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yajie Meng Min Jin Xianfang Tang Junlin Xu |
spellingShingle |
Yajie Meng Min Jin Xianfang Tang Junlin Xu Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease Associations IEEE Access miRNA-disease associations degree-based similarity indexes common neighbor and Jaccard area under curve (AUC) area under the precise recall curve (AUPR) |
author_facet |
Yajie Meng Min Jin Xianfang Tang Junlin Xu |
author_sort |
Yajie Meng |
title |
Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease Associations |
title_short |
Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease Associations |
title_full |
Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease Associations |
title_fullStr |
Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease Associations |
title_full_unstemmed |
Degree-Based Similarity Indexes for Identifying Potential miRNA-Disease Associations |
title_sort |
degree-based similarity indexes for identifying potential mirna-disease associations |
publisher |
IEEE |
series |
IEEE Access |
issn |
2169-3536 |
publishDate |
2020-01-01 |
description |
Identifying disease-associated miRNAs is helpful to explore the pathogenesis of diseases. However, without foreknowledge of the experimentally valid disease-associated miRNAs information, the development of promising and affordable approaches for effective treatment of human diseases is challenging. In this study, we develop DCNMDA and DJMDA, a degree-based similarity indexes methodology for identifying potential miRNAs-disease associations. We solely focused on the similarity and the degree between nodes without adopting negative samples or other external prior information beyond the miRNA-disease associations bipartite network. Trained on HMDD v2.0 and HMDD v3.0, DCNMDA achieved the highest AUCs (0.9237 and 0.9432, respectively) based on the 5-fold cross-validation and outperformed the published state-of-the-art methodologies. Moreover, case studies about breast neoplasms, lung neoplasms, and ovarian neoplasms further evaluate the reliability of the models. As a result, biological experiments can correspondingly verify 28 out of top-30 DJMDA-predicted MDAs and 29 out of top-30 DCNMDA-predicted MDAs. In summary, DCNMDA and DJMDA offer a powerful degree-based similarity index approach for identifying potential miRNAs-disease associations with superior performance. |
topic |
miRNA-disease associations degree-based similarity indexes common neighbor and Jaccard area under curve (AUC) area under the precise recall curve (AUPR) |
url |
https://ieeexplore.ieee.org/document/9133264/ |
work_keys_str_mv |
AT yajiemeng degreebasedsimilarityindexesforidentifyingpotentialmirnadiseaseassociations AT minjin degreebasedsimilarityindexesforidentifyingpotentialmirnadiseaseassociations AT xianfangtang degreebasedsimilarityindexesforidentifyingpotentialmirnadiseaseassociations AT junlinxu degreebasedsimilarityindexesforidentifyingpotentialmirnadiseaseassociations |
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