Whole Genome Messenger RNA Profiling Identifies a Novel Signature to Predict Gastric Cancer Survival.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30702489", "kind": "science-record", "revision": 8, "content_hash": "sha256:1a65477b6a7ff1f8bc41ea414abbb459a170c2c18e8cb3bf5ba33b5a4dc266e9", "created_at": "2026-11-01T15:40:41Z", "updated_at": "2026-11-01T22:00:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Whole Genome Messenger RNA Profiling Identifies a Novel Signature to Predict Gastric Cancer Survival.", "doi": "10.14309/ctg.0000000000000004", "pmid": "30702489", "authors": ["Jin Dai", "Zhe-Xuan Li", "Yang Zhang", "Jun-Ling Ma", "Tong Zhou", "Wei-Cheng You", "Wen-Qing Li", "Kai-Feng Pan"], "journal": "Clinical and translational gastroenterology", "year": 2019, "abstract": "OBJECTIVES: Molecular prognostic biomarkers for gastric cancer (GC) are still limited. We aimed to identify potential messenger RNAs (mRNAs) associated with GC prognosis and further establish an mRNA signature to predict the survival of GC based on the publicly accessible databases.\nMETHODS: Discovery of potential mRNAs associated with GC survival was undertaken for 441 patients with GC based on the Cancer Genome Atlas (TCGA), with information on clinical characteristics and vital status. Gene ontology functional enrichment analysis and pathway enrichment analysis were conducted to interrogate the possible biological functions. We narrowed down the list of mRNAs for validation study based on a significance level of 1.00 × 10, also integrating the information from the methylation analysis and constructing the protein-protein interaction network for elucidating biological processes. A total of 54 mRNAs were further studied in the validation stage, using the Gene Expression Omnibus (GEO) database (GSE84437, n = 433). The validated mRNAs were used to construct a risk score model predicting the prognosis of GC.\nRESULTS: A total of 13 mRNAs were significantly associated with survival of GC, after the validation stage, including DCLK1, FLRT2, MCC, PRICKLE1, RIMS1, SLC25A15, SLCO2A1, CDO1, GHR, CD109, SELP, UPK1B, and CD36. Except CD36, DCLK1, and SLCO2A1, other mRNAs are newly reported to be associated with GC survival. The 13 mRNA-based risk score had good performance on distinguishing GC prognosis, with a higher score indicating worse survival in both TCGA and GEO datasets.\nCONCLUSIONS: We established a 13-mRNA signature to potentially predict the prognosis of patients with GC, which might be useful in clinical practice for informing patient stratification.", "claims": [{"id": "claim-method", "statement": "Cox regression models were used to calculate the hazard ratios and 95% confidence intervals for the associations between each examined mRNA and GC death.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30702489", "locator": "sections[3] \"Screening mRNAs associated with GC survival in the discovery stage\" paragraph 3", "quote": "Cox regression models were used to calculate the hazard ratios and 95% confidence intervals for the associations between each examined mRNA and GC death."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data in the TCGA-STAD (stomach adenocarcinoma) training set, including clinical information, mRNA expression data, and DNA methylation profile, were downloaded from TCGA data portal (9).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30702489", "locator": "sections[3] \"Screening mRNAs associated with GC survival in the discovery stage\" paragraph 2", "quote": "All data in the TCGA-STAD (stomach adenocarcinoma) training set, including clinical information, mRNA expression data, and DNA methylation profile, were downloaded from TCGA data portal (9)."}], "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:30702489"], "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:30702489", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.14309/ctg.0000000000000004", "sha256": "sha256:b311d6d320604e179773e05f4551880a42f549c4788a58968e01a07d9195042d", "bytes": 29322, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.14309/ctg.0000000000000004", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6369880", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "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": "All data in the TCGA-STAD (stomach adenocarcinoma) training set, including clinical information, mRNA expression data, and DNA methylation profile, were downloaded from TCGA data portal (9).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data in the TCGA-STAD (stomach adenocarcinoma) training set, including clinical information, mRNA expression data, and DNA methylation profile, were downloaded from TCGA data portal (9).", "access_statement_kind": "repository_route_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", 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cancer death in TCGA and validated in GSE84437", "structure": {"pmcid": "PMC6369880", "section_index": 15, "section_title": "Selection of key candidate mRNAs for the validation study", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2.", "caption": "The HRs and P values for the association between 13 messenger RNAs and gastric cancer death in TCGA and validated in GSE84437", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[15]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-4", "family": null, "specific": null, "label": "Cox proportional hazard model", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Cox regression models were used to calculate the hazard ratios and 95% confidence intervals for the associations between each examined mRNA and GC death."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL 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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": ["All data in the TCGA-STAD (stomach adenocarcinoma) training set, including clinical information, mRNA expression data, and DNA methylation profile, were downloaded from TCGA data portal (9)."], "basis": "The paper names GSE84437 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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