Molecular Analysis of Prognosis and Immune Pathways of Pancreatic Cancer Based on TNF Family Members.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34630563", "kind": "science-record", "revision": 4, "content_hash": "sha256:2d5e4cebb0d7d7a7fdcd5fe75bff1b6190d0e0cee7dfd303266c9cd1d4e9c872", "created_at": "2026-11-01T17:36:16Z", "updated_at": "2026-11-01T22:04:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Molecular Analysis of Prognosis and Immune Pathways of Pancreatic Cancer Based on TNF Family Members.", "doi": "10.1155/2021/2676996", "pmid": "34630563", "authors": ["Zemin Zhu", "Caixi Tang", "Tao Xu", "Zhijian Zhao"], "journal": "Journal of oncology", "year": 2021, "abstract": "BACKGROUND: Tumor necrosis factor (TNF) family members play a vital role in anticancer therapy. This study aimed to screen the critical markers for the prognostic analysis of pancreatic adenocarcinoma (PAAD) by analyzing the clustering patterns of TNF family members in PAAD.\nMETHODS: In this study, the NMF clustering method was adopted to cluster samples from The Cancer Genome Atlas (TCGA) to acquire the clustering pattern of the TNF family in PAAD. Differential gene analysis was performed according to TNF family gene clusters. The support vector machine (SVM) method was conducted for further gene screening, and the risk score model of the screened genes was constructed by Lasso. The single sample gene set enrichment analysis (ssGSEA) method was adopted for immunoenrichment analysis and tumor immune cycle analysis. Genes associated with risk scores were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis.\nRESULTS: We clustered PAAD into two groups based on TNF family genes. Nineteen TNF family genes were significantly associated with the clinical characteristics of PAAD patients. The risk score formula was composed of RHOD, UBE2C, KLHDC7b, MSLN, ADAM8, NME3, GNG2, and MCOLN3. GSE57495 and GSE62452 datasets verified that patients in the high-risk group had a worse prognosis than those in the low-risk group. The risk score-related genes analyzed by GO and KEGG were mainly involved in the modulation of chemical synaptic transmission and synaptic vesicle cycle pathway. There were significant differences in the expression of 15 immune cells between the high-risk group and the low-risk group. The risk score was positively correlated with HCK, interferon, MHC-I, and STAT1. The expression of genes relevant to chemokine, immunostimulator, MHC, and receptor was strongly associated with the risk score.\nCONCLUSION: The risk score model based on the TNF family can predict the prognosis and immune status of PAAD patients. Further research is needed to verify the clinical prognostic value of risk scores.", "claims": [{"id": "claim-method", "statement": "In this study, the NMF clustering method was adopted to cluster samples from The Cancer Genome Atlas (TCGA) to acquire the clustering pattern of the TNF family in PAAD.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34630563", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In this study, the NMF clustering method was adopted to cluster samples from The Cancer Genome Atlas (TCGA) to acquire the clustering pattern of the TNF family in PAAD."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data supporting this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34630563", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "All data supporting this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The NMF clustering method clustered pancreatic adenocarcinoma patients into two groups based on TNF family gene expression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34630563", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We clustered PAAD into two groups based on TNF family genes."}, {"asset": "source:pmid:34630563", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In this study, the NMF clustering method was adopted to cluster samples from The Cancer Genome Atlas (TCGA) to acquire the clustering pattern of the TNF family in PAAD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The NMF clustering method clustered pancreatic adenocarcinoma patients into two groups based on TNF family gene expression.", "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:34630563"], "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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