Application of apoptosis-related genes in a multiomics-related prognostic model study of gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35991578", "kind": "science-record", "revision": 4, "content_hash": "sha256:eef00c06cdfbc08ecc383682d6c2c725af9fdbe31f11428f74768e8a05fde755", "created_at": "2026-11-01T18:15:08Z", "updated_at": "2026-11-01T22:07:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Application of apoptosis-related genes in a multiomics-related prognostic model study of gastric cancer.", "doi": "10.3389/fgene.2022.901200", "pmid": "35991578", "authors": ["Chengfei Xu", "Zilin Liu", "Chuanjing Yan", "Jiangwei Xiao"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Gastric cancer (GC) is one of the most common tumors in the world, and apoptosis is closely associated with GC. A number of therapeutic methods have been implemented to increase the survival in GC patients, but the outcomes remain unsatisfactory. Apoptosis is a highly conserved form of cell death, but aberrant regulation of the process also leads to a variety of major human diseases. As variations of apoptotic genes may increase susceptibility to gastric cancer. Thus, it is critical to identify novel and potent tools to predict the overall survival (OS) and treatment efficacy of GC. The expression profiles and clinical characteristics of TCGA-STAD and GSE15459 cohorts were downloaded from TCGA and GEO. Apoptotic genes were extracted from the GeneCards database. Apoptosis risk scores were constructed by combining Cox regression and LASSO regression. The GSE15459 and TCGA internal validation sets were used for external validation. Moreover, we explored the relationship between the apoptosis risk score and clinical characteristics, drug sensitivity, tumor microenvironment (TME) and tumor mutational burden (TMB). Finally, we used GSVA to further explore the signaling pathways associated with apoptosis risk. By performing TCGA-STAD differential analysis, we obtained 839 differentially expressed genes, which were then analyzed by Cox regressions and LASSO regression to establish 23 genes associated with apoptosis risk scores. We used the test validation cohort from TCGA-STAD and the GSE15459 dataset for external validation. The AUC values of the ROC curve for 2-, 3-, and 5-years survival were 0.7, 0.71, and 0.71 in the internal validation cohort from TCGA-STAD and 0.77, 0.74, and 0.75 in the GSE15459 dataset, respectively. We constructed a nomogram by combining the apoptosis risk signature and some clinical characteristics from TCGA-STAD. Analysis of apoptosis risk scores and clinical characteristics demonstrated notable differences in apoptosis risk scores between survival status, sex, grade, stage, and T stage. Finally, the apoptosis risk score was correlated with TME characteristics, drug sensitivity, TMB, and TIDE scores.", "claims": [{"id": "claim-method", "statement": "Apoptosis risk scores were constructed by combining Cox regression and LASSO regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35991578", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Apoptosis risk scores were constructed by combining Cox regression and LASSO regression."}], "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:35991578", "locator": "sections[24] \"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": "A 23-gene apoptosis risk score was constructed using Cox and LASSO regression and validated in TCGA-STAD and GSE15459, with reported AUC values indicating prognostic performance.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35991578", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "By performing TCGA-STAD differential analysis, we obtained 839 differentially expressed genes, which were then analyzed by Cox regressions and LASSO regression to establish 23 genes associated with apoptosis risk scores."}, {"asset": "source:pmid:35991578", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The AUC values of the ROC curve for 2-, 3-, and 5-years survival were 0.7, 0.71, and 0.71 in the internal validation cohort from TCGA-STAD and 0.77, 0.74, and 0.75 in the GSE15459 dataset, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A 23-gene apoptosis risk score was constructed using Cox and LASSO regression and validated in TCGA-STAD and GSE15459, with reported AUC values indicating prognostic performance.", "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:35991578"], "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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A number of t", "nts, but the outcomes remain unsatisfactory. Apoptosis is a highly conserved form of cell death, bu", "were extracted from the GeneCards database. Apoptosis risk scores were constructed by combining Co"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Apoptosis risk scores were constructed by combining Cox regression and LASSO regression."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}