Integrated analyses reveal the diagnostic and predictive values of COL5A2 and association with immune environment in Crohn's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38789829", "kind": "science-record", "revision": 4, "content_hash": "sha256:80d7b8bdd54c1e48e8bacb2ba75998faeac1fa71f1e6def3f6807f74179ba49e", "created_at": "2026-11-01T19:20:44Z", "updated_at": "2026-11-01T22:11:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated analyses reveal the diagnostic and predictive values of COL5A2 and association with immune environment in Crohn's disease.", "doi": "10.1038/s41435-024-00276-5", "pmid": "38789829", "authors": ["Tingting Zhong", "Xiaoqing Cheng", "Qianru Gu", "Guoxiang Fu", "Yihong Wang", "Yujie Jiang", "Jiaqi Xu", "Zhinong Jiang"], "journal": "Genes and immunity", "year": 2024, "abstract": "The pathogenesis of Crohn's disease (CD) involves abnormal immune cell infiltration and dysregulated immune response. Therefore, thorough research on immune cell abnormalities in CD is crucial for improved treatment of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained from the Gene Expression Omnibus (GEO) database. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) networks evaluated the proportion of immune infiltrating cells, constructed co-expression network and identified key genes, respectively. Based on the dataset (GSE134809), 15 cell clusters were defined and labeled as different cell types. Among the 11 modules, the yellow module had the closest relationship with plasma cells (cluster 5). Confirmed using RNA sequencing and IHC assay, the expression of COL5A2 in CD samples was higher than that in control samples. Furthermore, the COL5A2 protein expression remarkably decreased in the group of patients who responded to anti-tumor necrosis factor (TNF) treatments, compared to the non-response group. The comprehensive analyses described here provided novel insight into the landscape of CD-associated immune environment. In addition, COL5A2 were identified as potential diagnostic indicators for CD, as well as promising predictive markers for CD patients.", "claims": [{"id": "claim-method", "statement": "The receiver operating characteristic (ROC) curve was used to analyze the diagnostic and predictive value of gene expression in CD patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38789829", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "The receiver operating characteristic (ROC) curve was used to analyze the diagnostic and predictive value of gene expression in CD patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this research are available via public databases. The data and code that support the findings of this study are available from the corresponding author, upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38789829", "locator": "sections[28] \"notes\" paragraph 1", "quote": "The datasets used in this research are available via public databases. The data and code that support the findings of this study are available from the corresponding author, upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "COL5A2 and COL4A2 showed good diagnostic performance in CD, with AUC values of 0.83 and 0.88, respectively, when all GSE75214 mucosal samples were analyzed.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38789829", "locator": "sections[15] \"Diagnostic values of COL5A2 and COL4A2 in CD\" paragraph 2", "quote": "The area under the curve (AUC) values of COL5A2 and COL4A2 were 0.83 and 0.88, respectively, when all mucosal samples were conducted (Fig. 5A, B)."}, {"asset": "source:pmid:38789829", "locator": "sections[15] \"Diagnostic values of COL5A2 and COL4A2 in CD\" paragraph 3", "quote": "These findings indicated that the two key genes had good diagnostic performance in patients with CD, whether using ileum or colonic mucosal tissues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "COL5A2 and COL4A2 showed good diagnostic performance in CD, with AUC values of 0.83 and 0.88, respectively, when all GSE75214 mucosal samples were analyzed.", "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:38789829"], "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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Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were", "of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained f"], "order_basis": "paper_text_order:322", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["gle-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained from the Gene Expre", "roved treatment of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were", "th plasma cells (cluster 5). Confirmed using RNA sequencing and IHC assay, the expression of COL5A2 in C", "ne expression profiles were determined using RNA-Seq as previously described [26]. 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