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A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications
Disease–disease relationships (e.g., disease comorbidities) play crucial roles in pathobiological manifestations of diseases and personalized approaches to managing those conditions. In this study, we develop a network-based methodology, termed meta-path-based Disease Network (mpDisNet) capturing al...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853960/ https://www.ncbi.nlm.nih.gov/pubmed/31754458 http://dx.doi.org/10.1038/s41540-019-0115-2 |
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author | Jin, Shuting Zeng, Xiangxiang Fang, Jiansong Lin, Jiawei Chan, Stephen Y. Erzurum, Serpil C. Cheng, Feixiong |
author_facet | Jin, Shuting Zeng, Xiangxiang Fang, Jiansong Lin, Jiawei Chan, Stephen Y. Erzurum, Serpil C. Cheng, Feixiong |
author_sort | Jin, Shuting |
collection | PubMed |
description | Disease–disease relationships (e.g., disease comorbidities) play crucial roles in pathobiological manifestations of diseases and personalized approaches to managing those conditions. In this study, we develop a network-based methodology, termed meta-path-based Disease Network (mpDisNet) capturing algorithm, to infer disease–disease relationships by assembling four biological networks: disease–miRNA, miRNA–gene, disease–gene, and the human protein–protein interactome. mpDisNet is a meta-path-based random walk to reconstruct the heterogeneous neighbors of a given node. mpDisNet uses a heterogeneous skip-gram model to solve the network representation of the nodes. We find that mpDisNet reveals high performance in inferring clinically reported disease–disease relationships, outperforming that of traditional gene/miRNA-overlap approaches. In addition, mpDisNet identifies network-based comorbidities for pulmonary diseases driven by underlying miRNA-mediated pathobiological pathways (i.e., hsa-let-7a- or hsa-let-7b-mediated airway epithelial apoptosis and pro-inflammatory cytokine pathways) as derived from the human interactome network analysis. The mpDisNet offers a powerful tool for network-based identification of disease–disease relationships with miRNA-mediated pathobiological pathways. |
format | Online Article Text |
id | pubmed-6853960 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-68539602019-11-21 A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications Jin, Shuting Zeng, Xiangxiang Fang, Jiansong Lin, Jiawei Chan, Stephen Y. Erzurum, Serpil C. Cheng, Feixiong NPJ Syst Biol Appl Article Disease–disease relationships (e.g., disease comorbidities) play crucial roles in pathobiological manifestations of diseases and personalized approaches to managing those conditions. In this study, we develop a network-based methodology, termed meta-path-based Disease Network (mpDisNet) capturing algorithm, to infer disease–disease relationships by assembling four biological networks: disease–miRNA, miRNA–gene, disease–gene, and the human protein–protein interactome. mpDisNet is a meta-path-based random walk to reconstruct the heterogeneous neighbors of a given node. mpDisNet uses a heterogeneous skip-gram model to solve the network representation of the nodes. We find that mpDisNet reveals high performance in inferring clinically reported disease–disease relationships, outperforming that of traditional gene/miRNA-overlap approaches. In addition, mpDisNet identifies network-based comorbidities for pulmonary diseases driven by underlying miRNA-mediated pathobiological pathways (i.e., hsa-let-7a- or hsa-let-7b-mediated airway epithelial apoptosis and pro-inflammatory cytokine pathways) as derived from the human interactome network analysis. The mpDisNet offers a powerful tool for network-based identification of disease–disease relationships with miRNA-mediated pathobiological pathways. Nature Publishing Group UK 2019-11-13 /pmc/articles/PMC6853960/ /pubmed/31754458 http://dx.doi.org/10.1038/s41540-019-0115-2 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Jin, Shuting Zeng, Xiangxiang Fang, Jiansong Lin, Jiawei Chan, Stephen Y. Erzurum, Serpil C. Cheng, Feixiong A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications |
title | A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications |
title_full | A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications |
title_fullStr | A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications |
title_full_unstemmed | A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications |
title_short | A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications |
title_sort | network-based approach to uncover microrna-mediated disease comorbidities and potential pathobiological implications |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853960/ https://www.ncbi.nlm.nih.gov/pubmed/31754458 http://dx.doi.org/10.1038/s41540-019-0115-2 |
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