The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease
COPD (chronic obstructive pulmonary disease) and ILD (interstitial lung disease) are two common respiratory diseases. They share similar clinical traits but require different therapeutic treatments. Identifying the biomarkers that are differentially expressed between them will not only help the diag...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2019
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879656/ https://www.ncbi.nlm.nih.gov/pubmed/31824564 http://dx.doi.org/10.3389/fgene.2019.01154 |
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author | Yao, Yangwei Gu, Yangyang Yang, Meng Cao, Dakui Wu, Fengjie |
author_facet | Yao, Yangwei Gu, Yangyang Yang, Meng Cao, Dakui Wu, Fengjie |
author_sort | Yao, Yangwei |
collection | PubMed |
description | COPD (chronic obstructive pulmonary disease) and ILD (interstitial lung disease) are two common respiratory diseases. They share similar clinical traits but require different therapeutic treatments. Identifying the biomarkers that are differentially expressed between them will not only help the diagnosis of COPD and ILD, but also provide candidate drug targets that may facilitate the development of new treatment for COPD and ILD. Due to the irreversible complex pathological changes of COPD, there are very limited therapeutic options for COPD patients. In this study, we analyzed the gene expression profiles of two datasets: one training dataset that includes 144 COPD patients and 194 ILD patients, and one test dataset that includes 75 COPD patients and 61 ILD patients. Advanced feature selection methods, mRMR (minimal Redundancy Maximal Relevance) and incremental feature selection (IFS), were applied to identify the 38-gene biomarker. An SVM (support vector machine) classifier was built based on the 38-gene biomarker. Its accuracy, sensitivity, and specificity on training dataset evaluated by leave one out cross-validation were 0.905, 0.896, and 0.912, respectively. And on independent test dataset, the accuracy, sensitivity, and specificity on were as great as and were 0.904, 0.933, and 0.869, respectively. The biological function analysis of the 38 genes indicated that many of them can be potential treatment targets that may benefit COPD and ILD patients. |
format | Online Article Text |
id | pubmed-6879656 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-68796562019-12-10 The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease Yao, Yangwei Gu, Yangyang Yang, Meng Cao, Dakui Wu, Fengjie Front Genet Genetics COPD (chronic obstructive pulmonary disease) and ILD (interstitial lung disease) are two common respiratory diseases. They share similar clinical traits but require different therapeutic treatments. Identifying the biomarkers that are differentially expressed between them will not only help the diagnosis of COPD and ILD, but also provide candidate drug targets that may facilitate the development of new treatment for COPD and ILD. Due to the irreversible complex pathological changes of COPD, there are very limited therapeutic options for COPD patients. In this study, we analyzed the gene expression profiles of two datasets: one training dataset that includes 144 COPD patients and 194 ILD patients, and one test dataset that includes 75 COPD patients and 61 ILD patients. Advanced feature selection methods, mRMR (minimal Redundancy Maximal Relevance) and incremental feature selection (IFS), were applied to identify the 38-gene biomarker. An SVM (support vector machine) classifier was built based on the 38-gene biomarker. Its accuracy, sensitivity, and specificity on training dataset evaluated by leave one out cross-validation were 0.905, 0.896, and 0.912, respectively. And on independent test dataset, the accuracy, sensitivity, and specificity on were as great as and were 0.904, 0.933, and 0.869, respectively. The biological function analysis of the 38 genes indicated that many of them can be potential treatment targets that may benefit COPD and ILD patients. Frontiers Media S.A. 2019-11-20 /pmc/articles/PMC6879656/ /pubmed/31824564 http://dx.doi.org/10.3389/fgene.2019.01154 Text en Copyright © 2019 Yao, Gu, Yang, Cao and Wu http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Yao, Yangwei Gu, Yangyang Yang, Meng Cao, Dakui Wu, Fengjie The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease |
title | The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease |
title_full | The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease |
title_fullStr | The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease |
title_full_unstemmed | The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease |
title_short | The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease |
title_sort | gene expression biomarkers for chronic obstructive pulmonary disease and interstitial lung disease |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879656/ https://www.ncbi.nlm.nih.gov/pubmed/31824564 http://dx.doi.org/10.3389/fgene.2019.01154 |
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