Identification of an EMT-Related Gene Signature for Predicting Overall Survival in Gastric Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34249086", "kind": "science-record", "revision": 8, "content_hash": "sha256:8a64fa13c57dc8b290fdb2185dccd3c336cc51c8674bbded66e64b74593a43ff", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:47:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of an EMT-Related Gene Signature for Predicting Overall Survival in Gastric Cancer.", "doi": "10.3389/fgene.2021.661306", "pmid": "34249086", "authors": ["Weiyu Dai", "Yizhi Xiao", "Weimei Tang", "Jiaying Li", "Linjie Hong", "Jieming Zhang", "Miaomiao Pei", "Jianjiao Lin", "Side Liu", "Xiaosheng Wu", "Li Xiang", "Jide Wang"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "BACKGROUND: It has been widely reported that epithelial-mesenchymal transition (EMT) is associated with malignant progression in gastric cancer (GC). Integration of the molecules related to EMT for predicting overall survival (OS) is meaningful for understanding the role of EMT in GC. Here, we aimed to establish an EMT-related gene signature in GC.\nMETHODS: Transcriptional profiles and clinical data of GC were downloaded from The Cancer Genome Atlas (TCGA). We constructed EMT-related gene signature for predicting OS by using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. Time-dependent receiver operating characteristic (ROC), Kaplan-Meier analysis were performed to assess its predictive value. A nomogram combining the prognostic signature with clinical characteristics for OS prediction was established. And its predictive power was estimated by concordance index (C-index), time-dependent ROC curve, calibration curve and decision curve analysis (DCA). GSE62254 dataset from Gene Expression Omnibus (GEO) was used for external validation. Quantitative real-time PCR (qRT-PCR) was used to detected the mRNA expression of the five EMT-related genes in human normal gastric mucosal and GC cell lines. To further understand the potential mechanisms of the signature, Gene Set Enrichment Analysis (GSEA), pathway enrichment analysis, predictions of transcription factors (TFs)/miRNAs were performed.\nRESULTS: A novel EMT-related gene signature (including ITGAV, DAB2, SERPINE1, MATN3, PLOD2) was constructed for OS prediction of GC. With external validation, ROC curves indicated the signature's good performance. Patients stratified into high- and low-risk groups based on the signature yielded significantly different prognosis. Univariate and multivariate Cox regression suggested that the signature was an independent prognostic variable. Nomogram for prognostication including the signature presented better predictive accuracy and clinical usefulness than the similar model without risk score to some extent with external validation. The qRT-PCR assays suggested that high expression of the five EMT-related genes could be found in human GC cell lines compared with normal gastric mucosal cell line. GSEA and pathway enrichment analysis revealed that focal adhesion and ECM-receptor interaction might be the two important pathways to the signature.\nCONCLUSION: Our EMT-related gene signature may have practical application as an independent prognostic factor in GC.", "claims": [{"id": "claim-method", "statement": "All the survival analyses mentioned above were performed by Kaplan-Meier curve with a two-side log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249086", "locator": "sections[13] \"Survival Analysis\" paragraph 2", "quote": "All the survival analyses mentioned above were performed by Kaplan-Meier curve with a two-side log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA database: https://portal.gdc.cancer.gov/; GEO database: https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249086", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA database: https://portal.gdc.cancer.gov/; GEO database: https://www.ncbi.nlm.nih.gov/geo/."}], "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:34249086"], "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:GSE62254"], "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:GSE62254"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34249086", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2021.661306", "sha256": "sha256:3536d4abb8b0006693c556c07488c620c622e4dbee7c4de98deed3e5e5233c94", "bytes": 45307, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2021.661306", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8264558", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62254", "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=GSE62254", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62254", "version": null, "note": "Publicly available datasets were analyzed in this study. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:34249086", "data:geo:GSE62254", "asset:table:pmid:34249086:1", "asset:table:pmid:34249086:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62254"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34148, "completion_tokens": 3061, "cached_tokens": 11528}}, "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:34249086", "type": "paper", "label": "pmid:34249086"}, {"id": "source:pmid:34249086", "type": "manuscript", "label": "PMID 34249086 full text"}, {"id": "data:geo:GSE62254", "type": "dataset", "label": "GEO GSE62254"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34249086", "type": "paper", "label": "pmid:34249086"}, {"id": "source:pmid:34249086", "type": "manuscript", "label": "PMID 34249086 full text"}, {"id": "data:geo:GSE62254", "type": "dataset", "label": "GEO GSE62254"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34249086", "type": "extraction", "used": ["source:pmid:34249086"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62254", "type": "accession_resolution", "used": ["data:geo:GSE62254"], "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:34249086", "parent_hash": "sha256:26f3f269023e122a75138150d0394e479120e57df0b69a9f83e16fc409a95138", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE62254 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["s used for external validation. Quantitative real-time PCR (qRT-PCR) was used to detected the mRNA expr"], "order_basis": "paper_text_order:1177", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ine SNU-5 was obtained from ATCC. Cells were cultured in RPMI-1640 medium (Gibco, Grand Island, NY, U"], "order_basis": "paper_text_order:2959", "id": "assay:2"}, {"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": ["All the survival analyses mentioned above were performed by Kaplan-Meier curve with a two-side log-rank test."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}