Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects
Background and Objectives. Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airflow limitation. Although airway inflammation and oxidative stress are known to be important in the pathogenesis of COPD, the mechanism underlying airflow obstruction is not fully underst...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/206937 |
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| _version_ | 1832559077793726464 |
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| author | Woo Jin Kim Jae Hyun Lim Jae Seung Lee Sang-Do Lee Ju Han Kim Yeon-Mok Oh |
| author_facet | Woo Jin Kim Jae Hyun Lim Jae Seung Lee Sang-Do Lee Ju Han Kim Yeon-Mok Oh |
| author_sort | Woo Jin Kim |
| collection | DOAJ |
| description | Background and Objectives. Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airflow limitation. Although airway inflammation and oxidative stress are known to be important in the pathogenesis of COPD, the mechanism underlying airflow obstruction is not fully understood. Gene expression profiling of lung tissue was performed to define the molecular pathways that are dysregulated in COPD. Methods. RNA was isolated from lung tissues obtained from 98 subjects with COPD and 91 control subjects with normal spirometry. The RNA samples were processed with RNA-seq using the HiSeq 2000 system. Genes expressed differentially between the two groups were identified using Student’s t-test. Results. After filtering for genes with zero counts and noncoding genes, 16,676 genes were evaluated. A total of 2312 genes were differentially expressed between the lung tissues of COPD and control subjects (false discovery rate corrected q<0.01). The expression of genes related to oxidative phosphorylation and protein catabolism was reduced and genes related to chromatin modification were dysregulated in lung tissues of COPD subjects. Conclusions. Oxidative phosphorylation, protein degradation, and chromatin modification were the most dysregulated pathways in the lung tissues of COPD subjects. These findings may have clinical and mechanistic implications in COPD. |
| format | Article |
| id | doaj-art-679ef2091cf7410aae3346a62acc08a4 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-679ef2091cf7410aae3346a62acc08a42025-02-03T01:30:49ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/206937206937Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD SubjectsWoo Jin Kim0Jae Hyun Lim1Jae Seung Lee2Sang-Do Lee3Ju Han Kim4Yeon-Mok Oh5Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon National University, Chuncheon 200-722, Republic of KoreaSeoul National University Biomedical Informatics and Systems Biomedical Informatics Research Center, Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Republic of KoreaDepartment of Pulmonary and Critical Care Medicine, and Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of KoreaDepartment of Pulmonary and Critical Care Medicine, and Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of KoreaSeoul National University Biomedical Informatics and Systems Biomedical Informatics Research Center, Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Republic of KoreaDepartment of Pulmonary and Critical Care Medicine, and Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of KoreaBackground and Objectives. Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airflow limitation. Although airway inflammation and oxidative stress are known to be important in the pathogenesis of COPD, the mechanism underlying airflow obstruction is not fully understood. Gene expression profiling of lung tissue was performed to define the molecular pathways that are dysregulated in COPD. Methods. RNA was isolated from lung tissues obtained from 98 subjects with COPD and 91 control subjects with normal spirometry. The RNA samples were processed with RNA-seq using the HiSeq 2000 system. Genes expressed differentially between the two groups were identified using Student’s t-test. Results. After filtering for genes with zero counts and noncoding genes, 16,676 genes were evaluated. A total of 2312 genes were differentially expressed between the lung tissues of COPD and control subjects (false discovery rate corrected q<0.01). The expression of genes related to oxidative phosphorylation and protein catabolism was reduced and genes related to chromatin modification were dysregulated in lung tissues of COPD subjects. Conclusions. Oxidative phosphorylation, protein degradation, and chromatin modification were the most dysregulated pathways in the lung tissues of COPD subjects. These findings may have clinical and mechanistic implications in COPD.http://dx.doi.org/10.1155/2015/206937 |
| spellingShingle | Woo Jin Kim Jae Hyun Lim Jae Seung Lee Sang-Do Lee Ju Han Kim Yeon-Mok Oh Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects International Journal of Genomics |
| title | Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects |
| title_full | Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects |
| title_fullStr | Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects |
| title_full_unstemmed | Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects |
| title_short | Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects |
| title_sort | comprehensive analysis of transcriptome sequencing data in the lung tissues of copd subjects |
| url | http://dx.doi.org/10.1155/2015/206937 |
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