Identification of Differentially Expressed Genes Reveals BGN Predicting Overall Survival and Tumor Immune Infiltration of Gastric Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34868341", "kind": "science-record", "revision": 4, "content_hash": "sha256:ae025618878610d017beb1b1d2d36a52efdb7a6868751b2dfde0701fa3e79b63", "created_at": "2026-11-01T17:36:34Z", "updated_at": "2026-11-01T22:05:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Differentially Expressed Genes Reveals BGN Predicting Overall Survival and Tumor Immune Infiltration of Gastric Cancer.", "doi": "10.1155/2021/5494840", "pmid": "34868341", "authors": ["Weizhi Chen", "Zhongheng Yang"], "journal": "Computational and mathematical methods in medicine", "year": 2021, "abstract": "Gastric cancer (GC) is one of the most widely occurring malignancies worldwide. Although the diagnosis and treatment strategies of GC have been greatly improved in the past few decades, the morbidity and lethality rates of GC are still rising due to lacking early diagnosis strategies and powerful treatments. In this study, a total of 37 differentially expressed genes were identified in GC by analyzing TCGA, GSE118897, GSE19826, and GSE54129. Using the PPI database, we identified 17 hub genes in GC. By analyzing the expression of hub genes and OS, MFAP2, BGN, and TREM1 were related to the prognosis of GC. In addition, our results showed that higher levels of BGN exhibited a significant correlation with shorter OS time in GC. Nomogram analysis showed that the dysregulation of BGN could predict the prognosis of GC. Moreover, we revealed that BGN had a markedly negative correlation with B cells but had positive correlations with CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells in GC samples. The pan-cancer analysis demonstrated that BGN was differentially expressed and related to tumor-infiltrating immune cells across human cancers. This study for the first time comprehensively revealed that BGN was a potential biomarker for the prediction of GC prognosis and tumor immune infiltration.", "claims": [{"id": "claim-method", "statement": "The survival and survminer packages in R were employed to compare the OS between groups by Kaplan-Meier analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34868341", "locator": "sections[8] \"2.6. Survival Analysis\" paragraph 2", "quote": "The survival and survminer packages in R were employed to compare the OS between groups by Kaplan-Meier analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used during the present study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34868341", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The data used during the present study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "BGN achieved 1-, 3-, and 5-year AUC values of 0.536, 0.614, and 0.761 for predicting overall survival in gastric cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34868341", "locator": "sections[13] \"3.3. The Dysregulation of Hub Genes Was Correlated to Shorter Overall Survival (OS) Time in GC\" paragraph 2", "quote": "The 1-, 3-, and 5-year AUC values for the BGN were 0.536, 0.614, and 0.761 (Figure 2(h))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "BGN achieved 1-, 3-, and 5-year AUC values of 0.536, 0.614, and 0.761 for predicting overall survival in gastric cancer.", "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:34868341"], "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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