Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks

BACKGROUND: Since miRNAs can play important roles in different cancer types, how to discover cancer related miRNAs is an important issue. In general, the miRNAs with differential expression is the focus of attention. However, some important cancer related miRNAs are not excavated by differential exp...

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Detalles Bibliográficos
Autores principales: Pian, Cong, Zhang, Guangle, Wu, Sanling, Li, Fei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192342/
https://www.ncbi.nlm.nih.gov/pubmed/30326837
http://dx.doi.org/10.1186/s12859-018-2410-0
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author Pian, Cong
Zhang, Guangle
Wu, Sanling
Li, Fei
author_facet Pian, Cong
Zhang, Guangle
Wu, Sanling
Li, Fei
author_sort Pian, Cong
collection PubMed
description BACKGROUND: Since miRNAs can play important roles in different cancer types, how to discover cancer related miRNAs is an important issue. In general, the miRNAs with differential expression is the focus of attention. However, some important cancer related miRNAs are not excavated by differential expression analysis. We take this type of miRNAs as ‘dark matters’ (DM-miRNA). It is our great interests to develop an algorithm to discover DM-miRNAs. RESULTS: An effective method was developed to find DM-miRNAs. This method is mainly for mining potential DM-miRNAs by building basic miRNA-mRNA network (BMMN) and miRNA-lncRNA network (BMLN). The results indicate that miRNA-mRNA and miRNA-lncRNA interactions can be used as novel cancer biomarkers. CONCLUSIONS: The BMMN and BMLN can excavate the non-differentially expressed miRNAs which play an important role in the cancer. What’s more, the edge biomarkers (miRNA-mRNA and miRNA-lncRNA interactions) contain more information than the node biomarkers. It will contribute to developing novel therapeutic candidates in cancers. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2410-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-61923422018-10-22 Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks Pian, Cong Zhang, Guangle Wu, Sanling Li, Fei BMC Bioinformatics Research Article BACKGROUND: Since miRNAs can play important roles in different cancer types, how to discover cancer related miRNAs is an important issue. In general, the miRNAs with differential expression is the focus of attention. However, some important cancer related miRNAs are not excavated by differential expression analysis. We take this type of miRNAs as ‘dark matters’ (DM-miRNA). It is our great interests to develop an algorithm to discover DM-miRNAs. RESULTS: An effective method was developed to find DM-miRNAs. This method is mainly for mining potential DM-miRNAs by building basic miRNA-mRNA network (BMMN) and miRNA-lncRNA network (BMLN). The results indicate that miRNA-mRNA and miRNA-lncRNA interactions can be used as novel cancer biomarkers. CONCLUSIONS: The BMMN and BMLN can excavate the non-differentially expressed miRNAs which play an important role in the cancer. What’s more, the edge biomarkers (miRNA-mRNA and miRNA-lncRNA interactions) contain more information than the node biomarkers. It will contribute to developing novel therapeutic candidates in cancers. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2410-0) contains supplementary material, which is available to authorized users. BioMed Central 2018-10-16 /pmc/articles/PMC6192342/ /pubmed/30326837 http://dx.doi.org/10.1186/s12859-018-2410-0 Text en © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Pian, Cong
Zhang, Guangle
Wu, Sanling
Li, Fei
Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks
title Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks
title_full Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks
title_fullStr Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks
title_full_unstemmed Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks
title_short Discovering the ‘Dark matters’ in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks
title_sort discovering the ‘dark matters’ in expression data of mirna based on the mirna-mrna and mirna-lncrna networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192342/
https://www.ncbi.nlm.nih.gov/pubmed/30326837
http://dx.doi.org/10.1186/s12859-018-2410-0
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