A four-gene signature predicts overall survival of patients with esophageal adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38617513", "kind": "science-record", "revision": 3, "content_hash": "sha256:e9607f572895485505c2568c1d09cc4ffc081d176349b1bc28c2dcf5ae44adcc", "created_at": "2026-11-01T19:20:35Z", "updated_at": "2026-11-01T22:11:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A four-gene signature predicts overall survival of patients with esophageal adenocarcinoma.", "doi": "10.21037/tcr-23-1798", "pmid": "38617513", "authors": ["Yanmei Mao", "Haibo Zhang", "Xin He", "Jing Chen", "Lanyan Xi", "Yanping Chen", "Ying Zeng"], "journal": "Translational cancer research", "year": 2024, "abstract": "Background: Esophageal adenocarcinoma (EAC) is an aggressive cancer with poor prognosis. Thus, this study aimed to identify a prognostic molecular signature to predict the overall survival (OS) of patients with EAC.\nMethods: The mRNA microarray data sets GSE13898 and GSE26886 were downloaded from the Gene Expression Omnibus (GEO) database. RNA sequencing profile and clinical data of EAC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) between EAC tissues and adjacent non-cancerous tissues were obtained using R software. DEGs associated with prognosis of OS were assessed by univariate Cox analysis, and a prognostic signature was built using stepwise multivariate Cox analysis. Time-dependent receiver operating characteristic (ROC) analysis and stratification analysis were conducted to evaluate its predictive performance. Functional enrichment analysis was performed for genes co-expressed with the signature to explore its biological functions in EAC.\nResults: A total of 336 genes were identified to be differentially expressed between EAC tissues and adjacent non-cancerous tissues. After univariate and multivariate Cox regression analysis, four genes (ALAD, ABLIM3, IL17RB and IFI6) were screened out to construct a prognostic signature. According to this signature, patients could be assigned into high-risk and low-risk group with significantly different OS (P=4.92e-05<0.0001). Multivariate Cox regression analysis suggested that the four-gene signature served as an independent factor in OS prediction. In the time-dependent ROC analysis, the areas under the curves (AUCs) were 0.804, 0.792 and 0.695 for 1-, 3- and 5-year survival prediction, respectively, suggesting a good performance. Functional enrichment analysis showed that the signature was mainly clustered in cell proliferation related biological processes or pathways.\nConclusions: The four-gene signature identified in the current study may be a potential prognostic factor for predicting OS of EAC patients.", "claims": [{"id": "claim-data-access", "statement": "The mRNA microarray data sets GSE13898 and GSE26886 were downloaded from the Gene Expression Omnibus (GEO) database. The GSE13898 data set included 64 primary EAC tissues and 28 surrounding non-cancerous fresh frozen tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38617513", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mRNA microarray data sets GSE13898 and GSE26886 were downloaded from the Gene Expression Omnibus (GEO) database."}, {"asset": "source:pmid:38617513", "locator": "sections[4] \"Gene expression profiles of EAC\" paragraph 2", "quote": "The GSE13898 data set included 64 primary EAC tissues and 28 surrounding non-cancerous fresh frozen tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "According to this signature, patients could be assigned into high-risk and low-risk group with significantly different OS (P=4.92e−05<0.0001).", "kind": "quantitative", "target": {"value": 4.0, "unit": "p-value", "tolerance": null, "source": "According to this signature, patients could be assigned into high-risk and low-risk group with significantly different OS (P=4.92e−05<0.0001)."}, "evidence": [{"asset": "source:pmid:38617513", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "According to this signature, patients could be assigned into high-risk and low-risk group with significantly different OS (P=4.92e−05<0.0001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "According to this signature, patients could be assigned into high-risk and low-risk group with significantly different OS (P=4.92e−05<0.0001).", "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:38617513"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13898"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13898"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38617513", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-23-1798", "sha256": "sha256:4b68a032b6b86929da37e724ffc59ed2655a3a52bf11563437eb5cb4bea89bd6", "bytes": 39776, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-23-1798", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11009802", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13898", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13898", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13898", "version": null, "note": "The mRNA microarray data sets GSE13898 and GSE26886 were downloaded from the Gene Expression Omnibus (GEO) database. 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