Mining the key genes for ventilator-induced lung injury using co-expression network analysis
Autor: | Li Xu, Yajun Xiao, Zhao Li, Qingxiu Wang |
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Rok vydání: | 2021 |
Předmět: |
0301 basic medicine
R software VILI Key genes Microarray Bioinformatics Ventilator-Induced Lung Injury Respiratory System Biophysics Statistical difference Geo database Computational biology Lung injury Biology Biochemistry Mice 03 medical and health sciences 0302 clinical medicine Gene Modules Plasminogen Activator Inhibitor 1 Animals Gene Regulatory Networks Molecular Biology Gene Research Articles Activating Transcription Factor 3 Gene Expression & Regulation WGCNA Interleukins Pharmacology & Toxicology Computational Biology Membrane Proteins Cell Biology respiratory system Toll-Like Receptor 2 respiratory tract diseases 030104 developmental biology Matrix Metalloproteinase 9 Cyclooxygenase 2 030220 oncology & carcinogenesis Transcriptome Heme Oxygenase-1 |
Zdroj: | Bioscience Reports |
ISSN: | 1573-4935 0144-8463 |
Popis: | Mechanical ventilation is extensively adopted in general anesthesia and respiratory failure management, but it can also induce ventilator-induced lung injury (VILI). Therefore, it is of great urgency to explore the mechanisms involved in the VILI pathogenesis, which might contribute to its future prevention and treatment. Four microarray datasets from the GEO database were selected in our investigation, and were subjected to the Weighted Gene Co-Expression Network Analysis (WGCNA) to identify the VILI-correlated gene modules. The limma package in R software was used to identify the differentially expressed genes (DEGs) between the VILI and control groups. WGCNA was constructed by merging the GSE9314, GSE9368, GSE11434 and GSE11662 datasets. A total of 49 co-expression network modules were determined as associated with VILI. The intersected genes between hub genes screened from DEGs for VILI and those identified using WGCNA were as follows: Tlr2, Hmox1, Serpine1, Mmp9, Il6, Il1b, Ptgs2, Fos and Atf3, which were determined to be key genes for VILI. Those key genes were validated by GSE86229 and quantitative PCR (qPCR) experiment to have significantly statistical difference in their expression between the VILI and control groups. In a nutshell, nine key genes with expression differences in VILI were screened by WGCNA by integrating multiple datasets. |
Databáze: | OpenAIRE |
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