Identification and analysis of oxidative stress-related genes in hypoxic-ischemic brain damage using bioinformatics and experimental verification.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39172048", "kind": "science-record", "revision": 3, "content_hash": "sha256:b4729f0b30157c75f08912efa2cfd7f087d287973d0c19358831e77f85e1d4ab", "created_at": "2026-11-01T20:29:18Z", "updated_at": "2026-11-01T22:12:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and analysis of oxidative stress-related genes in hypoxic-ischemic brain damage using bioinformatics and experimental verification.", "doi": "10.1002/iid3.70000", "pmid": "39172048", "authors": ["Ni Jin", "Sha Sha", "Yanghao Ruan", "Ying Ouyang"], "journal": "Immunity, inflammation and disease", "year": 2024, "abstract": "BACKGROUND: Oxidative stress (OS) plays a major role in the progress of hypoxic-ischemic brain damage (HIBD). This study aimed to investigate OS-related genes and their underlying molecular mechanisms in neonatal HIBD.\nMETHODS: Microarray data sets were acquired from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) between control samples and HIBD samples. OS-related genes were drawn from GeneCards and OS-DEGs in HIBD were obtained by intersecting with the DEGs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were conducted to determine the underlying mechanisms and functions of OS-DEGs in HIBD. Moreover, the hub genes were screened using the protein-protein interaction network and identified in the GSE144456 data set. CIBERSORT was then performed to evaluate the expression of immunocytes in each sample and perform a correlation analysis of the optimal OS-DEGs and immunocytes. Finally, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunohistochemistry were performed to validate the expression levels of the optimal OS-DEGs.\nRESULTS: In total, 93 OS-DEGs were identified. GO, KEGG, and GSEA enrichment analyses indicated that these genes were predominantly enriched in OS and inflammation. Four OS-related biomarker genes (Jun, Fos, Tlr2, and Atf3) were identified and verified. CIBERSORT analysis revealed the dysregulation of six types of immune cells in the HIBD group. Moreover, 47 drugs that might target four OS-related biomarker genes were screened. Eventually, RT-qPCR and immunohistochemistry results for rat samples further validated the expression levels of Fos, Tlr2, and Atf3.\nCONCLUSIONS: Fos, Tlr2 and Atf3 are potential OS-related biomarkers of HIBD progression. The mechanisms of OS are associated with those of neonatal HIBD.", "claims": [{"id": "claim-method", "statement": "Furthermore, the correlation between immunocyte subgroups and gene expression levels were analyzed using Spearman's rank correlation in this study, and a heatmap of the correlation analysis between immune cells and the optimal OS‐DEGs was drawn.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39172048", "locator": "sections[7] \"Evaluation of immune cell infiltration\" paragraph 2", "quote": "Furthermore, the correlation between immunocyte subgroups and gene expression levels were analyzed using Spearman's rank correlation in this study, and a heatmap of the correlation analysis between immune cells and the optimal OS‐DEGs was drawn."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39172048", "locator": "sections[28] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are available from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Fos, Tlr2 and Atf3 are potential OS‐related biomarkers of HIBD progression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39172048", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Fos, Tlr2 and Atf3 are potential OS‐related biomarkers of HIBD progression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Fos, Tlr2 and Atf3 are potential OS‐related biomarkers of HIBD progression.", "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:39172048"], "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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