Identification and validation of hub genes expressed in ulcerative colitis with metabolic dysfunction-associated steatotic liver disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38550602", "kind": "science-record", "revision": 3, "content_hash": "sha256:e08b01c19ba1c71614c2303f660b0aebfa0f969373edfda8d8bd5d69fc7ffedc", "created_at": "2026-11-01T19:20:31Z", "updated_at": "2026-11-01T22:11:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of hub genes expressed in ulcerative colitis with metabolic dysfunction-associated steatotic liver disease.", "doi": "10.3389/fimmu.2024.1357632", "pmid": "38550602", "authors": ["Yupei Liu", "Jiao Li", "Shan Tian", "Qingzhi Lan", "Zhiyi Sun", "Chuan Liu", "Weiguo Dong"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Objective: Ulcerative colitis (UC) and metabolic dysfunction-associated steatotic liver disease (MASLD) are closely intertwined; however, the precise molecular mechanisms governing their coexistence remain unclear.\nMethods: We obtained UC (GSE75214) and MASLD (GSE151158) datasets from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were acquired by the 'edgeR' and 'limma' packages of R. We then performed functional enrichment analysis of common DEGs. Hub genes were selected using the cytoHubba plugin and validated using GSE87466 for UC and GSE33814 for MASLD. Immunohistochemistry was employed to validate the hub genes' expression in clinical samples. Immune infiltration and gene set enrichment analyses of the hub genes were performed. Finally, we estimated the Spearman's correlation coefficients for the clinical correlation of the core genes.\nResults: Within a cohort of 26 differentially regulated genes in both UC and MASLD, pathways involving cytokine-mediated signaling, cell chemotaxis, and leukocyte migration were enriched. After further validation, CXCR4, THY1, CCL20, and CD2 were identified as the hub genes. Analysis of immune infiltration patterns highlighted an association between elevated pivotal gene expression and M1 macrophage activation. Immunohistochemical staining revealed widespread expression of pivotal genes in UC- and MASLD-affected tissues. Furthermore, significant correlations were observed between the increased expression of hub genes and biochemical markers, such as albumin and prothrombin time.\nConclusion: This bioinformatics analysis highlights CXCR4, THY1, CCL20, and CD2 as crucial genes involved in the co-occurrence of UC and MASLD, providing insights into the underlying mechanisms of these two conditions.", "claims": [{"id": "claim-method", "statement": "The ‘pROC’ package was utilized to generate the receiver operating characteristic (ROC) curve, evaluating the ability of hub genes to differentiate between UC patients and healthy individuals across all datasets (20).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38550602", "locator": "sections[9] \"Construction of receiver-operating characteristic curves to assess diagnostic efficacy\" paragraph 2", "quote": "The ‘pROC’ package was utilized to generate the receiver operating characteristic (ROC) curve, evaluating the ability of hub genes to differentiate between UC patients and healthy individuals across all datasets (20)."}], "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:38550602", "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": "ROC analysis identified CXCR4, CCL20, THY1, and CD2 as promising diagnostic markers for UC and MASLD, with training-set AUCs of 0.890–0.932 for UC and 0.768–0.814 for MASLD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38550602", "locator": "sections[20] \"Using ROC curve to evaluate diagnostic efficacy in UC and MASLD\" paragraph 2", "quote": "In the UC training set, AUCs for CXCR4, CCL20, THY1, and CD2 hub genes were 0.903, 0.931, 0.932, and 0.890, respectively."}, {"asset": "source:pmid:38550602", "locator": "sections[20] \"Using ROC curve to evaluate diagnostic efficacy in UC and MASLD\" paragraph 2", "quote": "In the MASLD training set, the AUCs of the hub genes were 0.768, 0.802, 0.777, and 0.814, respectively."}, {"asset": "source:pmid:38550602", "locator": "sections[20] \"Using ROC curve to evaluate diagnostic efficacy in UC and MASLD\" paragraph 2", "quote": "These results indicate that CXCR4, CCL20, THY1, and CD2 are promising markers for the diagnosis of UC and MASLD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "ROC analysis identified CXCR4, CCL20, THY1, and CD2 as promising diagnostic markers for UC and MASLD, with training-set AUCs of 0.890–0.932 for UC and 0.768–0.814 for MASLD.", "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:38550602"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon", "step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38550602", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2024.1357632", "sha256": "sha256:e946bbd9d2a64e7c0f648de5996bdd24f69b301254769c28d015fc08b197bca9", "bytes": 54877, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2024.1357632", "version": null, "note": "Full article fetched from PMC; 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The datasets presented in this study can be found in online repositories. 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Immunohistochemistry was employed to validate the hub genes' expr", "ene expression and M1 macrophage activation. 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