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pmid:34247148
Clinical significance and prognostic role of an immune-related gene signature in gastric adenocarcinoma.
Rui Mao · Kehao Liu · Nana Zhao · Pengsen Guo · Yingxin Wu · Zheng Wang · Yanjun Liu · Tongtong Zhang
Aging · 2021 doi:10.18632/aging.203266
Paper
complete
Experiment
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Data
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Analysis
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Execution
absent
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Complete file
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The purpose of this study was to develop a reliable, personalized signature based on immune genes to predict the prognosis of GAC. Here, we identified two groups of patients with significantly different prognoses by performing unsupervised clustering analysis of The Cancer Genome Atlas (TCGA) database based on 881 immune genes. The immune signature was constructed with a training set composed of 350 GAC samples from the TCGA and subsequently validated with 431 samples from GSE84437, 432 samples from GSE26253, and 145 GAC samples from real-time quantitative reverse transcription polymerase chain reaction data. This classification system can also be used to predict prognosis in different clinical subgroups. Further analysis suggested that high-risk patients were characterized by low immune scores, distinctive immune cell proportions, different immune checkpoint profiles, and a low tumor mutational burden. Ultimately, the signature was identified as an independent prognostic factor. 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"", "", ""], ["I", "", "", "", "", "", "", ""], ["II", "0.1857", "1.5830", "0.8017-3.1280", "", "0.1553", "1.6560", "0.8260-3.3188"], ["III", "0.0144", "2.2300", "1.1734-4.2380", "", "0.0170", "2.2790", "1.1584-4.4817"], ["IV", "0.0004", "3.6980", "1.7921-7.6310", "", "0.0005", "3.8550", "1.7978-8.2680"], ["NA", "0.0002", "5.1930", "2.1954-12.2840", "", "0.0008", "4.7050", "1.9007-11.6448"], ["Grade", "", "", "", "", "", "", ""], ["1", "", "", "", "", "", "", ""], ["2", "0.4690", "1.6870", "0.4097-6.9480", "", "0.2812", "2.2500", "0.5148-9.8341"], ["3", "0.2910", "2.1300", "0.5240-8.6590", "", "0.1229", "3.2190", "0.7289-14.2170"], ["NA", "0.2280", "2.8420", "0.5201-15.5360", "", "0.0662", "5.4690", "0.8923-33.5155"], ["Risk score", "", "", "", "", "", "", ""], ["Increasing", "<0.0001", "2.4650", "1.7420-3.4880", "", "<0.0001", "2.3050", "1.5836-3.3562"]], "row_count": 27, "column_count": 8, "numeric_cells": 96, "header_rows": 0, "locator": "section[12]/table-wrap[1]#t2"}}, {"id": 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"parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE84437", "GSE26253"], "resolved_accessions": ["GSE84437", "GSE26253"], "statements": ["The data obtained from the TCGA and GEO datasets in this study are publicly available. Our research has been approved by the Institute of Oncology / Hospital Ethics Committee / Institutional Review Committee of Peking Union Medical College and the Chinese Academy of Medical Sciences (approval no. NCC2013RE-025)."], "basis": "The paper names GSE84437, GSE26253 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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