Analysis and application of RNA binding protein gene pairs to predict the prognosis of gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37539127", "kind": "science-record", "revision": 3, "content_hash": "sha256:7e866d97e4d9f1cb2997e78d3cf5a46e9d78bb4314c01739f967995db2a4fece", "created_at": "2026-11-01T19:02:19Z", "updated_at": "2026-11-01T22:10:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis and application of RNA binding protein gene pairs to predict the prognosis of gastric cancer.", "doi": "10.1016/j.heliyon.2023.e18242", "pmid": "37539127", "authors": ["Zhi-Kun Ning", "Hua-Kai Tian", "Jiang Liu", "Ce-Gui Hu", "Zi-Tao Liu", "Hui Li", "Zhen Zong"], "journal": "Heliyon", "year": 2023, "abstract": "Background: RNA-binding proteins (RBPs) are closely related to tumors, but little is known about the mechanism of RBPs in tumorigenesis and progression of gastric cancer (GC). As genes do not usually act alone in the pathway deregulation, gene pair combinations are more likely to become stable and accurate biomarkers. The purpose of our research is to establish a novel signature based on RBP gene pairs to predict the prognosis of gastric cancer patients.\nMethods: We downloaded genetic and clinical information from the TCGA and GEO database. TCGA and GSE13911 were used for screening differentially expressed genes (DEGs). The RBP genes were gathered from previous studies and employed to screen out DE-RBP genes after intersecting with DEGs. Samples were classified according to the relative expression of each pair of DE-RBP genes. The univariate Cox regression analysis and random forest were used to identify hub gene pairs to construct signature for predicting the prognosis of gastric cancer. Time-dependent ROC curves and KM survival curves were performed to evaluate the signature. GSEA was performed in TCGA training cohort and GSE62254 testing cohort to analyze enrichment pathways. Finally, the influence of these gene pairs on the prognosis of GC patients was further elucidated respectively through the combination of high and low expression of the two genes in each hub gene pair.\nResults: We screened out 6 hub RBP gene pairs (COL5A2/FEN1, POP1/GFRA1, EXO1/PLEKHS1, SLC39A10/CHI3L1, MMP7/PPP1R1 B and SLC5A6/BYSL) to predict the prognosis of patients with gastric cancer. Using the optimal cut-off value to divide patients into high-risk and low-risk groups in the training and testing cohort, we found that the overall survival (OS) of the low-risk group was higher than that of the high-risk group (P < 0.05). The area under the ROC curves for 1, 3, and 5 years were (0.659, 0.744, 0.758) and (0.624, 0.650, 0.653) in two cohorts. Univariate and multivariate Cox regression analysis showed that 6 RBP gene pairs signature were independent prognostic factors for gastric cancer (P < 0.05). In addition, the prognostic survival analysis showed that COL5A2-high/FEN1-low, POP1-low/GFRA1-high, EXO1-low/PLEKHS1-low,SLC39A10-high/CHI3L1-low, MMP7-high/PPP1R1 B-low, SLC5A6-low/BYSL-low had worse OS (P < 0.05). And the gene correlation analysis showed that there was no obvious correlation between the genes in each gene pairs except SLC5A6/BYSL and POP1/GFRA1. Finally, GSEA analysis showed that the high-risk group was enriched in tumor migration, invasion and growth-related pathways.\nConclusion: Our study identified a novel 6 RBP gene pairs signature to predict the prognosis of gastric cancer patients and provide potential targets for clinical gene therapy.", "claims": [{"id": "claim-method", "statement": "We performed univariate and multivariate Cox proportional-hazards analysis to identify independent prognostic factors using the “rms” R package in TCGA and GSE62254.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37539127", "locator": "sections[8] \"Independent prognostic factors\" paragraph 2", "quote": "We performed univariate and multivariate Cox proportional-hazards analysis to identify independent prognostic factors using the “rms” R package in TCGA and GSE62254."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors are unable or have chosen not to specify which data has been used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37539127", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The authors are unable or have chosen not to specify which data has been used."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our study identified a novel 6 RBP gene pairs signature to predict the prognosis of gastric cancer patients and provide potential targets for clinical gene therapy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37539127", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our study identified a novel 6 RBP gene pairs signature to predict the prognosis of gastric cancer patients and provide potential targets for clinical gene therapy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our study identified a novel 6 RBP gene pairs signature to predict the prognosis of gastric cancer patients and provide potential targets for clinical gene therapy.", "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:37539127"], "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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