Establishment and validation of a ubiquitination-related gene signature associated with prognosis in pancreatic duct adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37359528", "kind": "science-record", "revision": 3, "content_hash": "sha256:77fc8a46b9fdff3b794faee864ee2ad0503398e9f183add0bd0d1cca85e72f76", "created_at": "2026-11-01T19:02:06Z", "updated_at": "2026-11-01T22:09:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment and validation of a ubiquitination-related gene signature associated with prognosis in pancreatic duct adenocarcinoma.", "doi": "10.3389/fimmu.2023.1171811", "pmid": "37359528", "authors": ["Yangyang Guo", "Zhixuan Wu", "Kenan Cen", "Yongheng Bai", "Ying Dai", "Yifeng Mai", "Kai Hong", "Liangchen Qu"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Background: Patients with pancreatic duct adenocarcinoma (PDAC) have varied prognoses that depend on numerous variables. However, additional research is required to uncover the latent impact of ubiquitination-related genes (URGs) on determining PDAC patients' prognoses.\nMethods: The URGs clusters were discovered via consensus clustering, and the prognostic differentially expressed genes (DEGs) across clusters were utilized to develop a signature using a least absolute shrinkage and selection operator (LASSO) regression analysis of data from TCGA-PAAD. Verification analyses were conducted across TCGA-PAAD, GSE57495 and ICGC-PACA-AU to show the robustness of the signature. RT-qPCR was used to verify the expression of risk genes. Lastly, we formulated a nomogram to improve the clinical efficacy of our predictive tool.\nResults: The URGs signature, comprised of three genes, was developed and was shown to be highly correlated with the prognoses of PAAD patients. The nomogram was established by combining the URGs signature with clinicopathological characteristics. We discovered that the URGs signature was remarkably superior than other individual predictors (age, grade, T stage, et al). Also, the immune microenvironment analysis indicated that ESTIMATEscore, ImmuneScores, and StromalScores were elevated in the low-risk group. The immune cells that infiltrated the tissues were different between the two groups, as did the expression of immune-related genes.\nConclusion: The URGs signature could act as the biomarker of prognosis and selecting appropriate therapeutic drugs for PDAC patients.", "claims": [{"id": "claim-method", "statement": "Then, using multivariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses by “caret”, “glmnet” and “survival” packages, thress genes were selected and integrated into the prognostic signature (15).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37359528", "locator": "sections[5] \"Development and verification of the URGs prognostic signature\" paragraph 2", "quote": "Then, using multivariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses by “caret”, “glmnet” and “survival” packages, thress genes were selected and integrated into the prognostic signature (15)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37359528", "locator": "sections[22] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study developed a three-gene ubiquitination-related prognostic signature using LASSO regression with TCGA-PAAD as the source data.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37359528", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The URGs signature, comprised of three genes, was developed and was shown to be highly correlated with the prognoses of PAAD patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study developed a three-gene ubiquitination-related prognostic signature using LASSO regression with TCGA-PAAD as the source data.", "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:37359528"], "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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