Identification and validation of a novel ferroptosis-related gene model for predicting the prognosis of gastric cancer patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34252149", "kind": "science-record", "revision": 6, "content_hash": "sha256:aa65960ac78eb0f0d067b87d7e113c37e372bba5d84149c62ee3f18f418f37bd", "created_at": "2026-11-01T15:41:43Z", "updated_at": "2026-11-01T21:25:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of a novel ferroptosis-related gene model for predicting the prognosis of gastric cancer patients.", "doi": "10.1371/journal.pone.0254368", "pmid": "34252149", "authors": ["Gang Liu", "Jian-Ying Ma", "Gang Hu", "Huan Jin"], "journal": "PloS one", "year": 2021, "abstract": "BACKGROUND: Ferroptosis is a novel form of regulated cell death that plays a critical role in tumorigenesis. The purpose of this study was to establish a ferroptosis-associated gene (FRG) signature and assess its clinical outcome in gastric cancer (GC).\nMETHODS: Differentially expressed FRGs were identified using gene expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses were performed to construct a prognostic signature. The model was validated using an independent GEO dataset, and a genomic-clinicopathologic nomogram integrating risk scores and clinicopathological features was established.\nRESULTS: An 8-FRG signature was constructed to calculate the risk score and classify GC patients into two risk groups (high- and low-risk) according to the median value of the risk score. The signature showed a robust predictive capacity in the stratification analysis. A high-risk score was associated with advanced clinicopathological features and an unfavorable prognosis. The predictive accuracy of the signature was confirmed using an independent GSE84437 dataset. Patients in the two groups showed different enrichment of immune cells and immune-related pathways. Finally, we established a genomic-clinicopathologic nomogram (based on risk score, age, and tumor stage) to predict the overall survival (OS) of GC patients.\nCONCLUSIONS: The novel FRG signature may be a reliable tool for assisting clinicians in predicting the OS of GC patients and may facilitate personalized treatment.", "claims": [{"id": "claim-method", "statement": "The performance of the FRG signature for predicting OS was validated using ROC curves and Kaplan-Meier analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34252149", "locator": "sections[5] \"External validation of prognostic FRG signature\" paragraph 2", "quote": "The performance of the FRG signature for predicting OS was validated using ROC curves and Kaplan-Meier analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are available in the public databases TCGA database (http://www.cancer.gov/tcga) project TCGA-STAD, and Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/gds/) with the accession numbers: GSE84437.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34252149", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The datasets supporting the conclusions of this article are available in the public databases TCGA database (http://www.cancer.gov/tcga) project TCGA-STAD, and Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/gds/) with the accession numbers: GSE84437."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34252149"], "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:GSE84437"], "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:GSE84437"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34252149", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0254368", "sha256": "sha256:a82bb84e7203ba987cf30550d1e831d581e6e5030618eacf238f133f19edd623", "bytes": 45135, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0254368", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8274920", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84437", "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=GSE84437", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84437", "version": null, "note": "The datasets supporting the conclusions of this article are available in the public databases TCGA database (http://www.cancer.gov/tcga) project TCGA-STAD, and Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/gds/) with the accession numbers: GSE84437.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusions of this article are available in the public databases TCGA database (http://www.cancer.gov/tcga) project TCGA-STAD, and Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/gds/) with the accession numbers: GSE84437.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2235556", "GSM2235557", "GSM2235558", "GSM2235559", "GSM2235560", "GSM2235561", "GSM2235562", "GSM2235563", "GSM2235564", "GSM2235565", "GSM2235566", "GSM2235567", "GSM2235568", "GSM2235569", "GSM2235570", "GSM2235571", "GSM2235572", "GSM2235573", "GSM2235574", "GSM2235575", "GSM2235576", "GSM2235577", "GSM2235578", "GSM2235579", "GSM2235580", "GSM2235582", "GSM2235584", "GSM2235585", "GSM2235586", "GSM2235587", "GSM2235588", "GSM2235589", "GSM2235593", "GSM2235595", "GSM2235596", "GSM2235597", "GSM2235598", "GSM2235599", "GSM2235600", "GSM2235601", "GSM2235602", "GSM2235603", "GSM2235604", "GSM2235605", "GSM2235606", "GSM2235607", "GSM2235608", "GSM2235609", "GSM2235610", "GSM2235611", "GSM2235612", "GSM2235613", "GSM2235614", "GSM2235615", "GSM2235616", "GSM2235617", "GSM2235618", "GSM2235619", "GSM2235620", "GSM2235621", "GSM2235622", "GSM2235623", "GSM2235624", "GSM2235625", "GSM2235626", "GSM2235627", "GSM2235628", "GSM2235629", "GSM2235630", "GSM2235631", "GSM2235632", "GSM2235633", "GSM2235634", "GSM2235635", "GSM2235636", "GSM2235637", "GSM2235695", "GSM2235696", "GSM2235697", "GSM2235698", "GSM2235699", "GSM2235700", "GSM2235701", "GSM2235702", "GSM2235703", "GSM2235704", "GSM2235705", "GSM2235706", "GSM2235707", "GSM2235708", "GSM2235709", "GSM2235710", "GSM2235711", "GSM2235712", "GSM2235713", "GSM2235714", "GSM2235715", "GSM2235716", "GSM2235717", "GSM2235718", "GSM2235719", "GSM2235720", "GSM2235721", "GSM2235722", "GSM2235723", "GSM2235724", "GSM2235725", "GSM2235726", "GSM2235727", "GSM2235728", "GSM2235729", "GSM2235730", "GSM2235731", "GSM2235732", "GSM2235733", "GSM2235734", "GSM2235735", "GSM2235736", "GSM2235737", "GSM2235738", "GSM2235739", "GSM2235740", "GSM2235741", "GSM2235742", "GSM2235743", "GSM2235744", "GSM2235745", "GSM2235746", "GSM2235747", "GSM2235748", "GSM2235749", "GSM2235750", "GSM2235751", "GSM2235752", "GSM2235753", "GSM2235754", "GSM2235755", "GSM2235756", "GSM2235757", "GSM2235758", "GSM2235759", "GSM2235760", "GSM2235761", "GSM2235762", "GSM2235763", "GSM2235764", "GSM2235765", "GSM2235766", "GSM2235767", "GSM2235768", "GSM2235769", "GSM2235770", "GSM2235771", "GSM2235772", "GSM2235773", "GSM2235774", "GSM2235775", "GSM2235776", "GSM2235777", "GSM2235778", "GSM2235779", "GSM2235780", "GSM2235781", "GSM2235782", "GSM2235783", "GSM2235784", "GSM2235785", "GSM2235786", "GSM2235787", "GSM2235788", "GSM2235789", "GSM2235790", "GSM2235791", "GSM2235792", "GSM2235793", "GSM2235794", "GSM2235795", "GSM2235796", "GSM2235797", "GSM2235798", "GSM2235799", "GSM2235800", "GSM2235801", "GSM2235802", "GSM2235803", "GSM2235804", "GSM2235805", "GSM2235806", "GSM2235807", "GSM2235808", "GSM2235809", "GSM2235810", "GSM2235811", "GSM2235812", "GSM2235813", "GSM2235814", "GSM2235815", "GSM2235816", "GSM2235817", "GSM2235818", "GSM2235819", "GSM2235820", "GSM2235821", "GSM2235822", "GSM2235823", "GSM2235824", "GSM2235825", "GSM2235826", "GSM2235827", "GSM2235828", "GSM2235829", "GSM2235830", "GSM2235831", "GSM2235837", "GSM2235838", "GSM2235839", "GSM2235840", "GSM2235841", "GSM2235842", "GSM2235843", "GSM2235844", "GSM2235845", "GSM2235846", "GSM2235847", "GSM2235848", "GSM2235849", "GSM2235850", "GSM2235851", "GSM2235852", "GSM2235853", "GSM2235854", "GSM2235855", "GSM2235862", "GSM2235863", "GSM2235864", "GSM2235865", "GSM2235866", "GSM2235867", "GSM2235878", "GSM2235879", "GSM2235880", "GSM2235881", "GSM2235882", "GSM2235883", "GSM2235884", "GSM2235885", "GSM2235886", "GSM2235887", "GSM2235888", "GSM2235889", "GSM2235899", "GSM2235900", "GSM2235901", "GSM2235902", "GSM2235903", "GSM2235904", "GSM2235905", "GSM2235906", "GSM2235907", "GSM2235908", "GSM2235909", "GSM2235910", "GSM2235921", "GSM2235922", "GSM2235923", "GSM2235924", "GSM2235925", "GSM2235926", "GSM2235927", "GSM2235928", "GSM2235929", "GSM2235930", "GSM2235931", "GSM2235932", "GSM2235933", "GSM2235934", "GSM2235935", "GSM2235936", "GSM2235937", "GSM2235938", "GSM2235939", "GSM2235940", "GSM2235941", "GSM2235942", "GSM2235943", "GSM2235944", "GSM2235945", "GSM2235946", "GSM2235947", "GSM2235948", "GSM2235949", "GSM2235950", "GSM2235951", "GSM2235952", "GSM2235953", "GSM2235954", "GSM2235955", "GSM2235956", "GSM2235957", "GSM2235958", "GSM2235959", "GSM2235960", "GSM2235961", "GSM2235962", "GSM2235963", "GSM2235964", "GSM2235965", "GSM2235966", "GSM2235967", "GSM2235968", "GSM2235969", "GSM2235970", "GSM2235971", "GSM2235972", "GSM2235973", "GSM2235974", "GSM2235975", "GSM2235976", "GSM2235977", "GSM2235978", "GSM2235979", "GSM2235980", "GSM2235981", "GSM2235982", "GSM2235983", "GSM2235984", "GSM2235985", "GSM2235986", "GSM2235987", "GSM2235988", "GSM2235991", "GSM2235992", "GSM2235993", "GSM2235994", "GSM2235995", "GSM2235996", "GSM2235997", "GSM2235998", "GSM2235999", "GSM2236000", "GSM2236001", "GSM2236002", "GSM2236003", "GSM2236004", "GSM2236005", "GSM2236006", "GSM2236007", "GSM2236008", "GSM2236009", "GSM2236010", "GSM2236011", "GSM2236012", "GSM2236013", "GSM2236014", "GSM2236015", "GSM2236016", "GSM2236017", "GSM2236018", "GSM2236019", "GSM2236020", "GSM2236021", "GSM2236022", "GSM2236023", "GSM2236024", "GSM2236025", "GSM2236026", "GSM2236027", "GSM2236028", "GSM2236029", "GSM2236030", "GSM2236031", "GSM2236032", "GSM2236033", "GSM2236034", "GSM2236036", "GSM2236037", "GSM2236038", "GSM2236039", "GSM2236040", "GSM2236041", "GSM2236042", "GSM2236043", "GSM2236044", "GSM2236045", "GSM2236046", "GSM2236047", "GSM2236048", "GSM2236049", "GSM2236050", "GSM2236051", "GSM2236052", "GSM2236053", "GSM2236054", "GSM2236055", "GSM2236056", "GSM2236057", "GSM2236058", "GSM2236059", "GSM2236060", "GSM2236061", "GSM2236062", "GSM2236063", "GSM2236064", "GSM2236065", "GSM2236066", "GSM2236067", "GSM2236068", "GSM2236069", "GSM2236070", "GSM2236071", "GSM2236072", "GSM2236073", "GSM2236074", "GSM2236075", "GSM2236076", "GSM2236077", "GSM2236078", "GSM2236079", "GSM2236080", "GSM2236082", "GSM2236083", "GSM2236084", "GSM2236085", "GSM2236086", "GSM2236087", "GSM2236088", "GSM2236089", "GSM2236090", "GSM2236091", "GSM2236092", "GSM2236093", "GSM2236094", "GSM2236095", "GSM4419484", "GSM4419485", "GSM4419486", "GSM4419487", "GSM4419488", "GSM4419489", "GSM4419490", "GSM4419491", "GSM4419492", "GSM4419493", "GSM4419494", "GSM4419495", "GSM4419496", "GSM4419497", "GSM4419498", "GSM4419499", "GSM4419500", "GSM4419501", "GSM4419502", "GSM4419503", "GSM4419504", "GSM4419505", "GSM4419506", "GSM4419507", "GSM4419508", "GSM4419509", "GSM4419510", "GSM4419511", "GSM4419512", "GSM4419513", "GSM4419514", "GSM4419515", "GSM4419516", "GSM4419517", "GSM4419518", "GSM4419519", "GSM4419520", "GSM4419521", "GSM4419522", "GSM4419523", "GSM4419524", "GSM4419525", "GSM4419526", "GSM4419527", "GSM4419528", "GSM4419529", "GSM4419530", "GSM4419531", "GSM4419532", "GSM4419533"], "sample_count": 483, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34252149:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6ab5e01fdc0fccd049341d4d6085acea2227e14fb1b5f55954a4cfaf7c621b62", "bytes": 820, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone.0254368.t001", "version": null, "note": "Clinicopathologic characteristics of gastric cancer patients in TCGA and GEO cohorts.", "structure": {"pmcid": "PMC8274920", "section_index": 12, "section_title": "Clinicopathologic features of patients", "row_count": 21, "column_count": 3}, "table": {"label": "Table 1", "caption": "Clinicopathologic characteristics of gastric cancer patients in TCGA and GEO cohorts.", "rows": [["Variables", "TCGA cohort", "GEO cohort"], ["(n = 375)", "(n = 431)"], ["N (%)", "N (%)"], ["Age (M±SD, years)", "65.22±10.51", "60.02±11.58"], ["Age", "", ""], ["≤60", "125 (33.3)", "194 (28.3)"], ["> 60", "250 (66.7)", "237 (71.7)"], ["Gender", "", ""], ["Female", "135 (36.0)", "137 (45.5)"], ["Male", "240 (64.0)", "294 (54.5)"], ["Tumor location", "", ""], ["Cardia", "96 (25.6)", "/"], ["Non-cardia", "279 (74.4)", "/"], ["Grade", "", ""], ["G1-2", "140 (37.3)", "/"], ["G3", "235 (62.7)", "/"], ["Stage", "", ""], ["I", "47 (12.5)", "/"], ["II", "122 (32.5)", "/"], ["III", "172 (45.9)", "/"], ["IV", "34 (9.1)", "/"]], "row_count": 21, "column_count": 3, "numeric_cells": 23, "header_rows": 3, "locator": "section[12]/table-wrap[1]#pone.0254368.t001"}}], "gaps": ["asset:data:geo:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The performance of the FRG signature for predicting OS was validated using ROC curves and Kaplan-Meier analyses."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "Cox regression"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE84437"], "resolved_accessions": ["GSE84437"], "statements": ["The datasets supporting the conclusions of this article are available in the public databases TCGA database (http://www.cancer.gov/tcga) project TCGA-STAD, and Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/gds/) with the accession numbers: GSE84437."], "basis": "The paper names GSE84437 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:34252149", "data:geo:GSE84437", "asset:table:pmid:34252149:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE84437"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 36706, "completion_tokens": 2141, "cached_tokens": 715}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34252149", "type": "paper", "label": "pmid:34252149"}, {"id": "source:pmid:34252149", "type": "manuscript", "label": "PMID 34252149 full text"}, {"id": "data:geo:GSE84437", "type": "dataset", "label": "GEO GSE84437"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34252149", "type": "paper", "label": "pmid:34252149"}, {"id": "source:pmid:34252149", "type": "manuscript", "label": "PMID 34252149 full text"}, {"id": "data:geo:GSE84437", "type": "dataset", "label": "GEO GSE84437"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34252149", "type": "extraction", "used": ["source:pmid:34252149"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE84437", "type": "accession_resolution", "used": ["data:geo:GSE84437"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:34252149", "parent_hash": "sha256:af58ad5720159fa23c9fd0a97208c403d4ffd556b2c1db7dfa863acb9c4a54d1", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The performance of the FRG signature for predicting OS was validated using ROC curves and Kaplan-Meier analyses."], "order_basis": "analysis_only", "id": "assay:1"}]}