Identification and verification of ferroptosis-related genes in gastric intestinal metaplasia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37144125", "kind": "science-record", "revision": 4, "content_hash": "sha256:e19a0691865c60d5a06571abfe06bd186187d7de613678f1a23e1038e5ad0209", "created_at": "2026-11-01T19:01:48Z", "updated_at": "2026-11-01T22:51:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and verification of ferroptosis-related genes in gastric intestinal metaplasia.", "doi": "10.3389/fgene.2023.1152414", "pmid": "37144125", "authors": ["Biao Song", "Tingting Li", "Yi Zhang", "Qi Yang", "Bei Pei", "Yun Liu", "Jieyu Wang", "Gang Dong", "Qin Sun", "Shanshan Fan", "Xuejun Li"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: Gastric intestinal metaplasia (IM) is the key link of gastric precancerous lesions. Ferroptosis is a novel form of programmed cell death. However, its impact on IM is unclear. The focus of this study is to identify and verify ferroptosis-related genes (FRGs) that may be involved in IM by bioinformatics analysis. Materials and methods: Differentially expressed genes (DEGs) were obtained from microarray dataset GSE60427 and GSE78523 downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed ferroptosis-related genes (DEFRGs) were obtained from overlapping genes of DEGs and FRGs got from FerrDb. DAVID database was used for functional enrichment analysis. Protein-protein interaction (PPI) analysis and Cytoscape software were used to screen hub gene. In addition, we built a receiver operating characteristic (ROC) curve and verified the relative mRNA expression by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Finally, the CIBERSORT algorithm was used to analyze the immune infiltration in IM. Results: First, a total of 17 DEFRGs were identified. Second, a gene module identified by Cytoscape software was considered as hub gene: PTGS2, HMOX1, IFNG, and NOS2. Third, ROC analysis showed that HMOX1 and NOS2 had good diagnostic characteristics. qRT-PCR experiments confirmed the differential expression of HMOX1 in IM and normal gastric tissues. Finally, immunoassay showed that the proportion of T cells regulatory (Tregs) and macrophages M0 in IM was relatively higher, while the proportion of T cells CD4 memory activated and dendritic cells activated was lower. Conclusion: We found significant associations between FRGs and IM, and HMOX1 may be diagnostic biomarkers and therapeutic targets for IM. These results may enhance our understanding of IM and may contribute to its treatment.", "claims": [{"id": "claim-method", "statement": "The “limma” package in R software was used to screen differentially expressed genes (DEGs) between IM and normal subjects. The screening criterion was adjusted p < 0.05 and |log2FC| ≥ 1. We selected overlapping DEGs of FRGs as differently expressed ferroptosis-related genes (DEFRGs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37144125", "locator": "sections[4] \"2.2 Identification of differently expressed ferroptosis-related genes\" paragraph 2", "quote": "The “limma” package in R software was used to screen differentially expressed genes (DEGs) between IM and normal subjects. The screening criterion was adjusted p < 0.05 and |log2FC| ≥ 1. We selected overlapping DEGs of FRGs as differently expressed ferroptosis-related genes (DEFRGs)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/): GSE60427 and GSE78523; FerrDb database (http://www.zhounan.org/ferrdb); Kaplan-Meier Plotter database (http://kmplot.com/analysis/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37144125", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/): GSE60427 and GSE78523; FerrDb database (http://www.zhounan.org/ferrdb); Kaplan-Meier Plotter database (http://kmplot.com/analysis/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seventeen differentially expressed ferroptosis-related genes were identified, with PTGS2, HMOX1, IFNG, and NOS2 identified as hub genes, and HMOX1 and NOS2 showing good diagnostic characteristics for intestinal metaplasia.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37144125", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "First, a total of 17 DEFRGs were identified."}, {"asset": "source:pmid:37144125", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Second, a gene module identified by Cytoscape software was considered as hub gene: PTGS2, HMOX1, IFNG, and NOS2."}, {"asset": "source:pmid:37144125", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Third, ROC analysis showed that HMOX1 and NOS2 had good diagnostic characteristics."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seventeen differentially expressed ferroptosis-related genes were identified, with PTGS2, HMOX1, IFNG, and NOS2 identified as hub genes, and HMOX1 and NOS2 showing good diagnostic characteristics for intestinal metaplasia.", "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:37144125"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE60427"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE60427"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37144125", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2023.1152414", "sha256": "sha256:fe0d13aa1854693f9f7cfa105581760b9ba8831c9f77ad7a8a0db92b90cf9266", "bytes": 24463, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2023.1152414", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10151495", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE60427", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60427", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE60427", "version": null, "note": "Publicly available datasets were analyzed in this study. 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