Analysis of ferroptosis-associated genes in Crohn's disease based on bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36714107", "kind": "science-record", "revision": 4, "content_hash": "sha256:1515a04515bf8f64730ccc39205eae7a57ee6211afb73636ddded618a2eb3eab", "created_at": "2026-11-01T19:01:17Z", "updated_at": "2026-11-01T22:51:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of ferroptosis-associated genes in Crohn's disease based on bioinformatics.", "doi": "10.3389/fmed.2022.1058076", "pmid": "36714107", "authors": ["Xingyu Ji", "Su Ma", "Xiaomei Sun", "Dan Yu", "Ye Song", "Rui Li"], "journal": "Frontiers in medicine", "year": 2022, "abstract": "Background: Ferroptosis, a novel mode of apoptosis has recently been shown to be associated with fibrosis, tumor, cardiovascular, and other diseases. In this study, using bioinformatic analysis, we identified ferroptosis genes associated with Crohn's disease (CD) and performed biological function analysis, identified potential drug targets, and provided new directions for the future treatment of CD.\nMethods: Differential expression analysis was performed using the GSE186582 dataset from the Gene Expression Omnibus (GEO) database. Ferroptosis-associated genes were downloaded from the FerrDB database, and overlapping genes associated with CD and ferroptosis were extracted. Then, we performed functional enrichment analysis, constructed a protein-protein interaction network (PPI), identified the correlation between hub genes and immune infiltration, performed external validation using a second and third dataset (GSE102133, GSE95095), and identified potential therapeutic agents. Finally, we validated the protein expression levels of the identified hub genes by immunohistochemical staining in the colon tissues from CD and healthy participants.\nResults: A total of 28 ferroptosis-associated genes associated with CD were identified in our analysis, which included 22 up-regulated and 6 down-regulated genes. Gene Ontology (GO) analysis showed that these genes are essential for the apical plasma membrane and amide transport, and Metascape analysis showed that these genes mainly act on IL-4 and IL-13 signaling pathways. Five hub genes, PTGS2, IL6, IL1B, NOS2, and IDO1, were identified by a protein interaction network, and external validation of these hub genes showed statistically significant differences in expression between the CD patients and normal participants (p < 0.05), and all AUC values were greater than 0.8. Further, we predicted the top 10 drugs used to treat CD. Immune infiltration results suggest that Hub gene is related to T cells, macrophages, dendritic cells, and other immune cells. Finally, the results of immunohistochemical experiments showed that the protein expression of the hub gene was higher in CD colon tissue than in normal subjects (p < 0.05).\nConclusion: Bioinformatics analysis showed that ferroptosis is closely related to the development of CD, and the prediction of potential drugs provides new targets for the treatment of CD. Moreover, five hub genes identified are potentially new and effective markers for the diagnosis of CD.", "claims": [{"id": "claim-method", "statement": "For principal component analysis (PCA), the two R packages FactoMineR and factoextra were used and the LIMMA package was used for differential gene expression analysis. Differences in hub genes expression in CD and healthy samples were calculated using the t-test, and correlation analysis were calculated using Spearman analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36714107", "locator": "sections[5] \"2.3. Sample detection and differential gene analysis\" paragraph 2", "quote": "For principal component analysis (PCA), the two R packages FactoMineR and factoextra were used and the LIMMA package was used for differential gene expression analysis."}, {"asset": "source:pmid:36714107", "locator": "sections[13] \"2.11. Statistical analysis\" paragraph 2", "quote": "Differences in hub genes expression in CD and healthy samples were calculated using the t-test, and correlation analysis were calculated using Spearman analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36714107", "locator": "sections[25] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential-expression analysis of GSE186582 identified 649 differentially expressed genes in Crohn’s disease colon tissues compared with normal human colon tissues, including 316 up-regulated and 333 down-regulated genes.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "We found 649 genes differentially expressed (p < 0.05 and |log2 FC| > 1) in the colon of CD patients tissues compared with normal human colon tissues, of which 316 genes were up-regulated and 333 genes were down-regulated as shown in the volcano plot (Figure 1B)."}, "evidence": [{"asset": "source:pmid:36714107", "locator": "sections[15] \"3.1. Identification of differentially expressed genes\" paragraph 2", "quote": "We found 649 genes differentially expressed (p < 0.05 and |log2 FC| > 1) in the colon of CD patients tissues compared with normal human colon tissues, of which 316 genes were up-regulated and 333 genes were down-regulated as shown in the volcano plot (Figure 1B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential-expression analysis of GSE186582 identified 649 differentially expressed genes in Crohn’s disease colon tissues compared with normal human colon tissues, including 316 up-regulated and 333 down-regulated genes.", "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:36714107"], "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:GSE102133"], "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:GSE102133"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36714107", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2022.1058076", "sha256": "sha256:968f0466413f661f83ef8ad5ddb1992ed2fc7cabed335e3d78281073eb5c2813", "bytes": 50329, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2022.1058076", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9881725", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102133", "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=GSE102133", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102133", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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