Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease
Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizi...
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BioMed Central
2019-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2019-17-1-e2.pdf |
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| author | Seokjin Ham Yeon-Mok Oh Tae-Young Roh |
| author_facet | Seokjin Ham Yeon-Mok Oh Tae-Young Roh |
| author_sort | Seokjin Ham |
| collection | DOAJ |
| description | Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD. |
| format | Article |
| id | doaj-art-ed4e0a0088e54d4cb9c83967d2ce541e |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2019-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-ed4e0a0088e54d4cb9c83967d2ce541e2025-02-02T20:12:45ZengBioMed CentralGenomics & Informatics2234-07422019-03-0117110.5808/GI.2019.17.1.e2545Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary DiseaseSeokjin Ham0Yeon-Mok Oh1Tae-Young Roh2 Department of Life Sciences, POSTECH, Pohang 37674, Korea Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea Department of Life Sciences, POSTECH, Pohang 37674, KoreaChronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.http://genominfo.org/upload/pdf/gi-2019-17-1-e2.pdfchronic obstructive pulmonary diseasedeconvolutiongene co-expressiongene heterogeneityprotein sublocalization |
| spellingShingle | Seokjin Ham Yeon-Mok Oh Tae-Young Roh Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease Genomics & Informatics chronic obstructive pulmonary disease deconvolution gene co-expression gene heterogeneity protein sublocalization |
| title | Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease |
| title_full | Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease |
| title_fullStr | Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease |
| title_full_unstemmed | Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease |
| title_short | Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease |
| title_sort | evaluation and interpretation of transcriptome data underlying heterogeneous chronic obstructive pulmonary disease |
| topic | chronic obstructive pulmonary disease deconvolution gene co-expression gene heterogeneity protein sublocalization |
| url | http://genominfo.org/upload/pdf/gi-2019-17-1-e2.pdf |
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