Comprehensive analysis of abnormal expression, prognostic value and oncogenic role of the hub gene FN1 in pancreatic ductal adenocarcinoma via bioinformatic analysis and in vitro experiments.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34567847", "kind": "science-record", "revision": 7, "content_hash": "sha256:67521f7a335e5f1cde4caea5523b471391b532de1f67b7b24c08252754896a0d", "created_at": "2026-11-01T15:41:53Z", "updated_at": "2026-11-01T22:04:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of abnormal expression, prognostic value and oncogenic role of the hub gene FN1 in pancreatic ductal adenocarcinoma via bioinformatic analysis and in vitro experiments.", "doi": "10.7717/peerj.12141", "pmid": "34567847", "authors": ["Xiaohua Lei", "Guodong Chen", "Jiangtao Li", "Wu Wen", "Jian Gong", "Jie Fu"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is one of the most commonly diagnosed cancers with a poor prognosis worldwide. Although the treatment of PDAC has made great progress in recent years, the therapeutic effects are still unsatisfactory. Methods. In this study, we identified differentially expressed genes (DEGs) between PDAC and normal pancreatic tissues based on four Gene Expression Omnibus (GEO) datasets (GSE15471, GSE16515, GSE28735 and GSE71729). A protein-protein interaction (PPI) network was established to evaluate the relationship between the DEGs and to screen hub genes. The expression levels of the hub genes were further validated through the Gene Expression Profiling Interactive Analysis (GEPIA), ONCOMINE and Human Protein Atlas (HPA) databases, as well as the validation GEO dataset GSE62452. Additionally, the prognostic values of the hub genes were evaluated by Kaplan-Meier plotter and the validation GEO dataset GSE62452. Finally, the mechanistic roles of the most remarkable hub genes in PDAC were examined through in vitro experiments.\nRESULTS: We identified the following nine hub genes by performing an integrated bioinformatics analysis: COL1A1, COL1A2, FN1, ITGA2, KRT19, LCN2, MMP9, MUC1 and VCAN. All of the hub genes were significantly upregulated in PDAC tissues compared with normal pancreatic tissues. Two hub genes (FN1 and ITGA2) were associated with poor overall survival (OS) rates in PDAC patients. Finally, in vitro experiments indicated that FN1 plays vital roles in PDAC cell proliferation, colony formation, apoptosis and the cell cycle.\nCONCLUSIONS: In summary, we identified two hub genes that are associated with the expression and prognosis of PDAC. The oncogenic role of FN1 in PDAC was first illustrated by performing an integrated bioinformatic analysis and in vitro experiments. Our results provide a fundamental contribution for further research aimed finding novel therapeutic targets for overcoming PDAC.", "claims": [{"id": "claim-method", "statement": "The effects of the hub genes on overall survival (OS) were determined by the web-based Kaplan–Meier (KM) plotter tool (https://kmplot.com/analysis/) and the survival data of the validation dataset GSE62452. PDAC patients were divided into two groups (“High expression” and “Low expression”) based on the best cutoff calculated automatically. The hazard ratios (HR) with 95% confidence intervals and log rank P-values were calculated and are shown on the plot (Buddhan et al., 2007).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34567847", "locator": "sections[8] \"Survival analysis of the hub genes\" paragraph 2", "quote": "The effects of the hub genes on overall survival (OS) were determined by the web-based Kaplan–Meier (KM) plotter tool (https://kmplot.com/analysis/) and the survival data of the validation dataset GSE62452. PDAC patients were divided into two groups (“High expression” and “Low expression”) based on the best cutoff calculated automatically. 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CONCLUSIONS: In summary,"], "order_basis": "paper_text_order:1716", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lot (Buddhan et al., 2007). Cell culture and transfection The human PDAC cell lines PANC1 and SW1990 w", "e purchased from RiboBio (Guangzhou, China). Transfection was conducted by Lipofectamine 2,000 Reagent", "ntration of siFN1 is 100 nM. After 72 h, the transfected cells were harvested for further study. Stat", "RNAs (siRNAs) targeting FN1 and a scrambled siRNA used as a normal control (NC) were purchased"], "order_basis": "paper_text_order:2679", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["e Academy of Sciences (Shanghai, China). All cell lines were maintained in Dulbecco’s modified Eagle medium (HyClone"], "order_basis": "paper_text_order:2841", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The effects of the hub genes on overall survival (OS) were determined by the web-based Kaplan–Meier (KM) plotter tool (https://kmplot.com/analysis/) and the survival data of the validation dataset GSE62452. PDAC patients were divided into two groups (“High expression” and “Low expression”) based on the best cutoff calculated automatically. The hazard ratios (HR) with 95% confidence intervals and log rank P-values were calculated and are shown on the plot (Buddhan et al., 2007)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}