A long non-coding RNA signature to improve prognosis prediction of gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27647437", "kind": "science-record", "revision": 6, "content_hash": "sha256:402e7f8af7a890f3a63ad3e03826f2632c0129c856c9ce4da3f7fc822f247a21", "created_at": "2026-11-01T15:40:20Z", "updated_at": "2026-11-01T21:20:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A long non-coding RNA signature to improve prognosis prediction of gastric cancer.", "doi": "10.1186/s12943-016-0544-0", "pmid": "27647437", "authors": ["Xiaoqiang Zhu", "Xianglong Tian", "Chenyang Yu", "Chaoqin Shen", "Tingting Yan", "Jie Hong", "Zheng Wang", "Jing-Yuan Fang", "Haoyan Chen"], "journal": "Molecular cancer", "year": 2016, "abstract": "BACKGROUND: Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis. We aimed at developing alncRNA signature to improve prognosis prediction of gastric cancer (GC).\nMETHODS: Using a lncRNA-mining approach, we performed lncRNA expression profiling in large GC cohorts from Gene Expression Ominus (GEO), including GSE62254 data set (N = 300) and GSE15459 data set (N = 192). We established a set of 24-lncRNAs that were significantly associated with the disease free survival (DFS) in the test series.\nRESULTS: Based on this 24-lncRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different DFS (HR = 1.19, 95 % CI = 1.13-1.25, P < 0.0001). The prognostic value of this 24-lncRNA signature was confirmed in the internal validation series and another external validation series, respectively. Further analysis revealed that the prognostic value of this signature was independent of lymph node ratio (LNR) and postoperative chemotherapy. Gene set enrichment analysis (GSEA) indicated that high risk score group was associated with several cancer recurrence and metastasis associated pathways.\nCONCLUSIONS: The identification of the prognostic lncRNAs indicates the potential roles of lncRNAs in GC biogenesis. Our results may provide an efficient classification tool for clinical prognosis evaluation of GC.", "claims": [{"id": "claim-method", "statement": "Those 63 genes were further analyzed by random survival forest-variable hunting (RSF-VH) algorithm [36].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27647437", "locator": "sections[9] \"Identification of prognostic lncRNA genes from the test series\" paragraph 2", "quote": "Those 63 genes were further analyzed by random survival forest-variable hunting (RSF-VH) algorithm [36]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE62254 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62254) and GSE15459 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15459).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27647437", "locator": "sections[26] \"ack\" paragraph 1", "quote": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE62254 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62254) and GSE15459 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15459)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A 24-lncRNA signature developed using sample splitting, random survival forests-variable hunting, and Cox regression from GEO microarray cohorts stratified gastric cancer patients into high- and low-risk groups with significantly different disease-free survival (HR = 1.19, 95% CI = 1.13–1.25, P < 0.0001).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Based on this 24-lncRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different DFS (HR = 1.19, 95 % CI = 1.13–1.25, P < 0.0001)."}, "evidence": [{"asset": "source:pmid:27647437", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Based on this 24-lncRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different DFS (HR = 1.19, 95 % CI = 1.13–1.25, P < 0.0001)."}, {"asset": "source:pmid:27647437", "locator": "sections[1] \"Background\" paragraph 4", "quote": "By using the sample-splitting method, random survival forests-variable hunting (RSF-VH) algorithm and Cox regression analysis, we identified a prognostic, 24-lncRNA signature from the GSE62254 test series patients, and validated it in the GSE62254 validation series and another independent GEO cohort (GSE15459)."}, {"asset": "source:pmid:27647437", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using a lncRNA-mining approach, we performed lncRNA expression profiling in large GC cohorts from Gene Expression Ominus (GEO), including GSE62254 data set (N = 300) and GSE15459 data set (N = 192)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A 24-lncRNA signature developed using sample splitting, random survival forests-variable hunting, and Cox regression from GEO microarray cohorts stratified gastric cancer patients into high- and low-risk groups with significantly different disease-free survival (HR = 1.19, 95% CI = 1.13–1.25, P < 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:27647437"], "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:GSE15459"], "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:GSE15459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27647437", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12943-016-0544-0", "sha256": 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identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study [gastric tumors]", "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:27647437:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c023961bc941229aa7d481fa0cbcccc2db62f7ea759d755a8f63135682e0cabf", "bytes": 2888, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab1", "version": null, "note": "LncRNAs significantly associated with the disease free survival in the test series patients (N = 180)", "structure": {"pmcid": "PMC5029104", "section_index": 9, "section_title": "Identification of prognostic lncRNA genes from the test series", "row_count": 25, "column_count": 8}, "table": {"label": "Table 1", "caption": "LncRNAs significantly associated with the disease free survival in the test series patients (N = 180)", "rows": [["Probe", "Gene symbol", "Permutation P valuea,b", "Hazard ratioa", "Coefficienta", "VI", "Associated diseases", "Description"], ["233512_at", "AF035291", "0.0017", "8.325", "2.11846", "0.012", "NR", "hypothetical LOC100287216"], ["1568854_at", "AI028608", "0.0084", "6.839", "1.92247", "−0.002", "NR", "non-protein coding RNA 240"], ["229280_s_at", "AK026189", "6.00E-04", "4.633", "1.53266", "0.006", "Melanoma and basal cell carcinoma", "promotes metastasis and recurrence of melanoma"], ["1559412_at", "H04858", "8.00E-04", "4.030", "1.3926", "0.002", "Acute megakaryoblastic leukemia", "Maintenance of leukemic growth"], ["1559965_at", "BC037827", "0.0018", "3.587", "1.27718", "0.053", "NR", "hypothetical LOC100192378"], ["1557338_x_at", "BC038210", "0.0108", "3.326", "1.20171", "0.017", "NR", "NR"], ["230589_at", "AI916498", "0.0034", "2.844", "1.04591", "−0.006", "Gastric cancer", "Sensitivity of iodine-125 particle irradiation and regulation of NF-KB signaling pathway"], ["239466_at", "AA463827", "0.0013", "2.799", "1.0294", "0.026", "NR", "hypothetical LOC344595"], ["230251_at", "AA041523", "0.0014", "2.521", "0.92436", "0.038", "Non-small cell lung cancer", "Associated with loss function of LKB1 gene"], ["225029_at", "BE621082", "0.0016", "2.249", "0.81047", "0.007", "Systemic lupus erythematosus", "A novel susceptibility locus on Xp11.21"], ["1564139_at", "AK056852", "0.0016", "1.923", "0.65369", "0.004", "NR", "hypothetical LOC144571"], ["229014_at", "AW206234", "0.0021", "1.718", "0.54056", "0.002", "NR", "hypothetical LOC441094"], ["1558828_s_at", "AL703532", "0.0032", "1.325", "0.2811", "0.005", "Heart failure associated diseases", "Regulation of cardiac cell differentiation and homeostasis"], ["235759_at", "AI095542", "0.0034", "1.282", "0.24825", "−0.004", "NR", "NR"], ["213972_at", "AI080288", "0.0036", "0.155", "−1.86125", "−0.007", "NR", "NR"], ["1554880_at", "BC021187", "0.0024", "0.106", "−2.24862", "−0.002", "Gastric cancer", "Protective roles for gastric cancer"], ["235824_at", "BF238392", "0.0019", "0.073", "−2.61423", "0.012", "NR", "NR"], ["232191_at", "BC005107", "0.0076", "0.070", "−2.65478", "0.002", "NR", "chromosome 21 open reading frame 105"], ["1563296_at", "BC039674", "0.0022", "0.068", "−2.69258", "0.000", "NR", "NR"], ["239617_at", "AI056187", "9.00E-04", "0.061", "−2.79863", "−0.001", "Gastric cancer", "spans the promoter and untranslated regions\\of the ghrelin gene"], ["243975_at", "T79746", "0.0031", "0.058", "−2.85076", "0.003", "NR", "NR"], ["1558666_at", "H11436", "3.00E-04", "0.055", "−2.89127", "−0.007", "NR", "NR"], ["237471_at", "BF511694", "0.0034", "0.041", "−3.19733", "0.003", "NR", "hypothetical LOC154822"], ["1562683_a_at", "BC035722", "0.0023", "0.033", "−3.40924", "0.001", "NR", "hypothetical LOC285547"]], "row_count": 25, "column_count": 8, "numeric_cells": 155, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:27647437:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:16fc4747ecc3967e4fe45454c8199ee6ac6af6d1db81a395e7a0b447b2c57a23", "bytes": 1074, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab2", "version": null, "note": "Multivariable Cox regression analysis of the 24-lncRNA risk score, LNR and postoperative chemotherapy in GSE62254 series", "structure": {"pmcid": "PMC5029104", "section_index": 13, "section_title": "Prognostic value of the 24-lncRNA signature is independent of LNR", "row_count": 17, "column_count": 4}, "table": {"label": "Table 2", "caption": "Multivariable Cox regression analysis of the 24-lncRNA risk score, LNR and postoperative chemotherapy in GSE62254 series", "rows": [["Variables", "HR", "95 % CI of HR", "P value"], ["24-lncRNA risk score (N = 300)", "1.16", "1.10 –1.21", "<0.0001"], ["LNR", "4.33", "1.34 –13.93", "0.014"], ["Age", "1.03", "1.00 –1.05", "0.032"], ["Gender", "1.10", "0.65 –1.84", "0.732"], ["TNM stage I", "1.00(referent)", "", ""], ["TNM stage II", "1.08", "0.23 –5.08", "0.919"], ["TNM stage III", "2.09", "0.47 –9.24", "0.330"], ["TNM stage IV", "3.89", "0.82 –18.44", "0.087"], ["24-lncRNA risk score (N = 299)", "1.14", "1.09 –1.19", "< 0.0001"], ["Postoperative chemotherapy", "0.36", "0.18 –0.73", "0.004"], ["Age", "1.01", "0.99 –1.03", "0.324"], ["Gender", "1.04", "0.62 –1.75", "0.897"], ["TNM stage I", "1.00(referent)", "", ""], ["TNM stage II", "1.47", "0.31 –6.85", "0.626"], ["TNM stage III", "4.00", "0.93 –17.15", "0.062"], ["TNM stage IV", "8.50", "2.00 –36.20", "0.004"]], "row_count": 17, "column_count": 4, "numeric_cells": 47, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE62254 licence not read"]}, "analysis": {"state": "partial", "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": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"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": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": null, "specific": null, "label": "Random survival forest-variable hunting (RSF-VH) algorithm", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Those 63 genes were further analyzed by random survival forest-variable hunting (RSF-VH) algorithm [36]."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-hazard-ratio", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 1.19, "unit": "hazard ratio", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 0.0001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["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": ["GSE62254", "GSE15459"], "resolved_accessions": ["GSE62254", "GSE15459"], "statements": ["The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE62254 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62254) and GSE15459 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15459)."], "basis": "The paper names GSE62254, GSE15459 in Gene Expression Omnibus and the accession resolves in the repository. 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