Cargando…

Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph

One key issue in the post-genomic era is how to systematically describe the associations between small molecule transcripts or translations inside cells. With the rapid development of high-throughput “omics” technologies, the achieved ability to detect and characterize molecules with other molecule...

Descripción completa

Detalles Bibliográficos
Autores principales: Guo, Zhen-Hao, Yi, Hai-Cheng, You, Zhu-Hong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6721720/
https://www.ncbi.nlm.nih.gov/pubmed/31405040
http://dx.doi.org/10.3390/cells8080866
_version_ 1783448406193078272
author Guo, Zhen-Hao
Yi, Hai-Cheng
You, Zhu-Hong
author_facet Guo, Zhen-Hao
Yi, Hai-Cheng
You, Zhu-Hong
author_sort Guo, Zhen-Hao
collection PubMed
description One key issue in the post-genomic era is how to systematically describe the associations between small molecule transcripts or translations inside cells. With the rapid development of high-throughput “omics” technologies, the achieved ability to detect and characterize molecules with other molecule targets opens the possibility of investigating the relationships between different molecules from a global perspective. In this article, a molecular association network (MAN) is constructed and comprehensively analyzed by integrating the associations among miRNA, lncRNA, protein, drug, and disease, in which any kind of potential associations can be predicted. More specifically, each node in MAN can be represented as a vector by combining two kinds of information including the attribute of the node itself (e.g., sequences of ncRNAs and proteins, semantics of diseases and molecular fingerprints of drugs) and the behavior of the node in the complex network (associations with other nodes). A random forest classifier is trained to classify and predict new interactions or associations between biomolecules. In the experiment, the proposed method achieved a superb performance with an area under curve (AUC) of 0.9735 under a five-fold cross-validation, which showed that the proposed method could provide new insight for exploration of the molecular mechanisms of disease and valuable clues for disease treatment.
format Online
Article
Text
id pubmed-6721720
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-67217202019-09-10 Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph Guo, Zhen-Hao Yi, Hai-Cheng You, Zhu-Hong Cells Article One key issue in the post-genomic era is how to systematically describe the associations between small molecule transcripts or translations inside cells. With the rapid development of high-throughput “omics” technologies, the achieved ability to detect and characterize molecules with other molecule targets opens the possibility of investigating the relationships between different molecules from a global perspective. In this article, a molecular association network (MAN) is constructed and comprehensively analyzed by integrating the associations among miRNA, lncRNA, protein, drug, and disease, in which any kind of potential associations can be predicted. More specifically, each node in MAN can be represented as a vector by combining two kinds of information including the attribute of the node itself (e.g., sequences of ncRNAs and proteins, semantics of diseases and molecular fingerprints of drugs) and the behavior of the node in the complex network (associations with other nodes). A random forest classifier is trained to classify and predict new interactions or associations between biomolecules. In the experiment, the proposed method achieved a superb performance with an area under curve (AUC) of 0.9735 under a five-fold cross-validation, which showed that the proposed method could provide new insight for exploration of the molecular mechanisms of disease and valuable clues for disease treatment. MDPI 2019-08-09 /pmc/articles/PMC6721720/ /pubmed/31405040 http://dx.doi.org/10.3390/cells8080866 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Guo, Zhen-Hao
Yi, Hai-Cheng
You, Zhu-Hong
Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph
title Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph
title_full Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph
title_fullStr Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph
title_full_unstemmed Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph
title_short Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph
title_sort construction and comprehensive analysis of a molecular association network via lncrna–mirna–disease–drug–protein graph
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6721720/
https://www.ncbi.nlm.nih.gov/pubmed/31405040
http://dx.doi.org/10.3390/cells8080866
work_keys_str_mv AT guozhenhao constructionandcomprehensiveanalysisofamolecularassociationnetworkvialncrnamirnadiseasedrugproteingraph
AT yihaicheng constructionandcomprehensiveanalysisofamolecularassociationnetworkvialncrnamirnadiseasedrugproteingraph
AT youzhuhong constructionandcomprehensiveanalysisofamolecularassociationnetworkvialncrnamirnadiseasedrugproteingraph