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Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer
Integrating high-throughput data obtained from different molecular levels is essential for understanding the mechanisms of complex diseases such as cancer. In this study, we integrated the methylation, microRNA and mRNA data from lung cancer tissues and normal lung tissues using functional gene sets...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422260/ https://www.ncbi.nlm.nih.gov/pubmed/22912875 http://dx.doi.org/10.1371/journal.pone.0043441 |
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author | Huang, Tao Jiang, Min Kong, Xiangyin Cai, Yu-Dong |
author_facet | Huang, Tao Jiang, Min Kong, Xiangyin Cai, Yu-Dong |
author_sort | Huang, Tao |
collection | PubMed |
description | Integrating high-throughput data obtained from different molecular levels is essential for understanding the mechanisms of complex diseases such as cancer. In this study, we integrated the methylation, microRNA and mRNA data from lung cancer tissues and normal lung tissues using functional gene sets. For each Gene Ontology (GO) term, three sets were defined: the methylation set, the microRNA set and the mRNA set. The discriminating ability of each gene set was represented by the Matthews correlation coefficient (MCC), as evaluated by leave-one-out cross-validation (LOOCV). Next, the MCCs in the methylation sets, the microRNA sets and the mRNA sets were ranked. By comparing the MCC ranks of methylation, microRNA and mRNA for each GO term, we classified the GO sets into six groups and identified the dysfunctional methylation, microRNA and mRNA gene sets in lung cancer. Our results provide a systematic view of the functional alterations during tumorigenesis that may help to elucidate the mechanisms of lung cancer and lead to improved treatments for patients. |
format | Online Article Text |
id | pubmed-3422260 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-34222602012-08-21 Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer Huang, Tao Jiang, Min Kong, Xiangyin Cai, Yu-Dong PLoS One Research Article Integrating high-throughput data obtained from different molecular levels is essential for understanding the mechanisms of complex diseases such as cancer. In this study, we integrated the methylation, microRNA and mRNA data from lung cancer tissues and normal lung tissues using functional gene sets. For each Gene Ontology (GO) term, three sets were defined: the methylation set, the microRNA set and the mRNA set. The discriminating ability of each gene set was represented by the Matthews correlation coefficient (MCC), as evaluated by leave-one-out cross-validation (LOOCV). Next, the MCCs in the methylation sets, the microRNA sets and the mRNA sets were ranked. By comparing the MCC ranks of methylation, microRNA and mRNA for each GO term, we classified the GO sets into six groups and identified the dysfunctional methylation, microRNA and mRNA gene sets in lung cancer. Our results provide a systematic view of the functional alterations during tumorigenesis that may help to elucidate the mechanisms of lung cancer and lead to improved treatments for patients. Public Library of Science 2012-08-17 /pmc/articles/PMC3422260/ /pubmed/22912875 http://dx.doi.org/10.1371/journal.pone.0043441 Text en © 2012 Huang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Huang, Tao Jiang, Min Kong, Xiangyin Cai, Yu-Dong Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer |
title | Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer |
title_full | Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer |
title_fullStr | Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer |
title_full_unstemmed | Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer |
title_short | Dysfunctions Associated with Methylation, MicroRNA Expression and Gene Expression in Lung Cancer |
title_sort | dysfunctions associated with methylation, microrna expression and gene expression in lung cancer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422260/ https://www.ncbi.nlm.nih.gov/pubmed/22912875 http://dx.doi.org/10.1371/journal.pone.0043441 |
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