Underlying Molecular Mechanism and Construction of a miRNA-Gene Network in Idiopathic Pulmonary Fibrosis by Bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37686108", "kind": "science-record", "revision": 3, "content_hash": "sha256:12d89b849705975813119cb0923435a06bb6a83f71c55f96971ef2c1b6d2841d", "created_at": "2026-11-01T19:02:29Z", "updated_at": "2026-11-01T22:10:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Underlying Molecular Mechanism and Construction of a miRNA-Gene Network in Idiopathic Pulmonary Fibrosis by Bioinformatics.", "doi": "10.3390/ijms241713305", "pmid": "37686108", "authors": ["Shuping Zheng", "Yan Zhang", "Yangfan Hou", "Hongxin Li", "Jin He", "Hongyan Zhao", "Xiuzhen Sun", "Yun Liu"], "journal": "International journal of molecular sciences", "year": 2023, "abstract": "Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease, but its pathogenesis is still unclear. Bioinformatics methods were used to explore the differentially expressed genes (DEGs) and to elucidate the pathogenesis of IPF at the genetic level. The microarray datasets GSE110147 and GSE53845 were downloaded from the Gene Expression Omnibus (GEO) database and analyzed using GEO2R to obtain the DEGs. The DEGs were further analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genomes (KEGG) pathway enrichment using the DAVID database. Then, using the STRING database and Cytoscape, a protein-protein interaction (PPI) network was created and the hub genes were selected. In addition, lung tissue from a mouse model was validated. Lastly, the network between the target microRNAs (miRNAs) and the hub genes was constructed with NetworkAnalyst. A summary of 240 genes were identified as DEGs, and functional analysis highlighted their role in cell adhesion molecules and ECM-receptor interactions in IPF. In addition, eight hub genes were selected. Four of these hub genes (VCAM1, CDH2, SPP1, and POSTN) were screened for animal validation. The IHC and RT-qPCR of lung tissue from a mouse model confirmed the results above. Then, miR-181b-5p, miR-4262, and miR-155-5p were predicted as possible key miRNAs. Eight hub genes may play a key role in the development of IPF. Four of the hub genes were validated in animal experiments. MiR-181b-5p, miR-4262, and miR-155-5p may be involved in the pathophysiological processes of IPF by interacting with hub genes.", "claims": [{"id": "claim-method", "statement": "To identify DEGs in IPF compared to normal tissue, GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r, accessed on 20 February 2023) was applied (|logFC| ≥ 1 and adj. p ≤ 0.01).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37686108", "locator": "sections[12] \"4.2. DEGs Screening and Data Processing\" paragraph 2", "quote": "To identify DEGs in IPF compared to normal tissue, GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r, accessed on 20 February 2023) was applied (|logFC| ≥ 1 and adj. p ≤ 0.01)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data will be made available on request. The data that support the findings of this study are available from the corresponding author, Dr. Liu, upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37686108", "locator": "sections[27] \"notes\" paragraph 1", "quote": "Data will be made available on request. The data that support the findings of this study are available from the corresponding author, Dr. Liu, upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GEO2R analysis of GSE110147 and GSE53845 identified 240 overlapping differentially expressed genes between IPF and normal lung tissue.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37686108", "locator": "sections[3] \"2.1. The Identification of DEGs\" paragraph 2", "quote": "After standardization of the microarray results, analysis was performed using the GEO2R."}, {"asset": "source:pmid:37686108", "locator": "sections[3] \"2.1. The Identification of DEGs\" paragraph 2", "quote": "As displayed in the Venn diagram (Figure 1G) between IPF and normal lung tissue, the overlapping of the two datasets included 240 genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GEO2R analysis of GSE110147 and GSE53845 identified 240 overlapping differentially expressed genes between IPF and normal lung tissue.", "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:37686108"], "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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