Mining the key genes for ventilator-induced lung injury using co-expression network analysis.

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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.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed based on the merged expression profiling data, and DEGs were identified using the limma package for R, under the condition of adj P<0.05 and |log2FC|>1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33687057", "locator": "sections[6] \"Identification of DEGs\" paragraph 2", "quote": "Differential expression analysis was performed based on the merged expression profiling data, and DEGs were identified using the limma package for R, under the condition of adj P<0.05 and |log2FC|>1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used and/or analyzed in the present study are available in the GEO database (https://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33687057", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The data used and/or analyzed in the present study are available in the GEO database (https://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33687057"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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