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pmid:30288103
An expression signature model to predict lung adenocarcinoma-specific survival.
Xiaoshun Shi · Haoming Tan · Xiaobing Le · Haibing Xian · Xiaoxiang Li · Kailing Huang · Viola Yingjun Luo · Yanhui Liu · Zhuolin Wu · Haiyun Mo · Allen M Chen · Ying Liang · Jiexia Zhang
Cancer management and research · 2018 doi:10.2147/CMAR.S159563
Paper
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Experiment
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Data
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Analysis
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30288103", "kind": "science-record", "revision": 7, "content_hash": "sha256:30db750d178964d702f7a7f7d368ecb808d33d9f11abc8378cd3e24cccb8ead3", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T22:00:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An expression signature model to predict lung adenocarcinoma-specific survival.", "doi": "10.2147/CMAR.S159563", "pmid": "30288103", "authors": ["Xiaoshun Shi", "Haoming Tan", "Xiaobing Le", "Haibing Xian", "Xiaoxiang Li", "Kailing Huang", "Viola Yingjun Luo", "Yanhui Liu", "Zhuolin Wu", "Haiyun Mo", "Allen M Chen", "Ying Liang", "Jiexia Zhang"], "journal": "Cancer management and research", "year": 2018, "abstract": "BACKGROUND: The current TNM staging system plays a central role in lung adenocarcinoma (LUAD) prognosis. However, it may not adequately stratify the risk of tumor recurrence. With the aid of gene expression profiling, we identified 31 lncRNAs whose expressions in tumor tissues could be used as a risk indicator for the guidance of lung cancer therapy. This exploratory analysis may shed new light on identification of potential prognostic factors.\nMATERIALS AND METHODS: A survival prediction scoring model was developed from the data that are publicly available in The Cancer Genome Atlas (TCGA) LUAD RNA Sequencing dataset. Multivariate Cox regression analysis and Kaplan-Meier analysis were performed on a cohort of 254 stage I lung carcinoma patients with survival records.\nRESULTS: Our model indicates that the panels comprising 31 lncRNAs are highly associated with overall survival (OS): 18.9% (95% CI: 10.4%-34.5%) and 89.5% (95% CI: 80.7%-99.2%) for the high- and low-risk group, respectively. The specificity and sensitivity of the model are verified, which show that the area under receiver operating characteristic curve yields 0.881, meaning our model has good accuracy and it is feasible for further applications.\nCONCLUSION: The 31-lncRNA model might be able to predict OS in patients with LUAD with high accuracy. Its further applications in biomolecular experiments using clinical samples with independent cohorts of patients are needed to verify the results.", "claims": [{"id": "claim-method", "statement": "Cox multivariate analysis was employed to test whether the risk score was independent of potential clinical risk factors including age, gender, smoking history and disease stage.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30288103", "locator": "sections[6] \"Risk score and survival curve\" paragraph 2", "quote": "Cox multivariate analysis was employed to test whether the risk score was independent of potential clinical risk factors including age, gender, smoking history and disease stage."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are enclosed in this article and the supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30288103", "locator": "sections[14] \"Availability of data and material\" paragraph 2", "quote": "All data generated or analyzed during this study are enclosed in this article and the supplementary information files."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:30288103"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30288103", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S159563", "sha256": "sha256:1b22fef5c57887f7370b3bb586703e1d3334fb7bbb3331aa1b6cf5641202d5a0", "bytes": 92051, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S159563", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6161724", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:30288103:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d190f4eb26d1c8f093f72a3e3bd44831fe9cd544afc116b2e5b317e6596f367", "bytes": 2530, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t1-cmar-10-3717", "version": null, "note": "31-lncRNA risk score model", "structure": {"pmcid": "PMC6161724", "section_index": 6, 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"access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#ts1-cmar-10-3717", "version": null, "note": "Differentially expressed lncRNAs", "structure": {"pmcid": "PMC6161724", "section_index": 15, "section_title": "Supplementary materials", "row_count": 347, "column_count": 7}, "table": {"label": "Table S1", "caption": "Differentially expressed lncRNAs", "rows": [["ID", "Normal mean", "LUAD mean", "Fold change", "log2 fold change", "pval", "padj"], ["FENDRR", "2981.044549", "202.0454063", "0.067776715", "−3.88306647965706", "2.06E-58", "2.35E-55"], ["C14orf132", "4536.086751", "729.8425231", "0.16089695", "−2.635791116862", "1.26E-36", "4.41E-34"], ["LINC01272", "2806.558749", "499.3803316", "0.177933326", "−2.49059135320854", "2.22E-26", "4.10E-24"], ["RP3-340N1.2", "8.089904837", "537.0428035", "66.38431655", "6.052770537", "1.41E-22", "1.94E-20"], ["RP11-88I21.2", "158.625216", "5.082194866", "0.03203901", 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"327.0135833", "29.48115008", "0.090152677", "−3.4714858515193", "5.48E-13", "2.61E-11"], ["RP11-805I24.3", "77.73713493", "4.591115755", "0.059059493", "−4.08168722493331", "7.25E-13", "3.42E-11"], ["MIR3945HG", "257.2013858", "21.76416665", "0.084619166", "−3.56287173018701", "8.24E-13", "3.83E-11"], ["PVT1", "109.9042973", "731.3404474", "6.65433896", "2.734295356", "1.61E-12", "7.22E-11"], ["LINC01314", "581.6797822", "66.86203392", "0.114946464", "−3.12096601344235", "3.42E-12", "1.48E-10"], ["CASC9", "3.877102467", "177.2081692", "45.70634146", "5.514322439", "3.74E-12", "1.61E-10"], ["LINC00665", "225.0598783", "1100.560291", "4.890077697", "2.289857388", "5.82E-12", "2.46E-10"], ["LINC01082", "42.576707", "2.270463438", "0.053326422", "−4.22900566210113", "9.14E-12", "3.78E-10"], ["AC011286.1", "18.26333348", "0.75709458", "0.041454348", "−4.59233276424982", "1.90E-11", "7.58E-10"], ["AC128709.2", "35.80940814", "1.7201411", "0.04803601", "−4.37973985796622", "3.36E-11", "1.28E-09"], ["AC109642.1", "701.5189391", "129.6115514", "0.184758449", "−2.43628775194037", "4.68E-11", "1.73E-09"], ["RP11-401P9.4", "736.6771455", "152.074051", "0.206432427", "−2.27625848393677", "6.33E-11", "2.32E-09"], ["RP11-89K21.1", "0.764187204", "80.81937877", "105.758613", "6.724631351", "9.96E-11", "3.54E-09"], ["RP5-839B4.8", "302.5155357", "37.5504844", "0.124127458", "−3.01010581056547", "3.03E-10", "1.00E-08"], ["RP11-81H3.2", "0.332099875", "49.41633002", "148.7996044", "7.217226881", "6.11E-10", "1.93E-08"], ["CH17-360D5.2", "501.2718126", "85.9882572", "0.17154018", "−2.54338155142695", "2.02E-09", "5.82E-08"], ["CTD-2139B15.5", "0.049962099", "25.1743678", "503.8692964", "8.976905737", "2.84E-09", "7.97E-08"], ["LINC00551", "114.7444773", "13.63409013", "0.118821319", "−3.07313438771013", "6.51E-09", "1.73E-07"], ["LINC01552", "42.82576179", "4.110438691", "0.095980515", "−3.38111462894993", "6.91E-09", "1.83E-07"], ["LINC00973", "1.121767602", "82.0215184", 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"row_count": 61, "column_count": 7}, "table": {"label": "Table S2", "caption": "Univariate Cox regression result", "rows": [["ID", "Coefficient", "HR", "95% lower confidence limit", "95% upper confidence limit", "z-score", "Pr(>|z-score|)"], ["RP11-434D9.1", "−0.0966741972375059", "0.907851739", "0.872852909", "0.944253918", "−4.81960124604818", "1.44E-06"], ["RP11-497G19.2", "−0.0473439461021022", "0.953759299", "0.932661358", "0.975334502", "−4.14823078202511", "3.35E-05"], ["LINC00518", "0.062426122", "1.064415819", "1.033004562", "1.096782218", "4.084624611", "4.41E-05"], ["CCAT1", "0.061524925", "1.063457002", "1.032176397", "1.095685582", "4.039030045", "5.37E-05"], ["LINC01352", "−0.0775259586521217", "0.925403002", "0.891074473", "0.961054033", "−4.01965107946729", "5.83E-05"], ["AC109642.1", "−0.198604826848537", "0.819873821", "0.742542429", "0.90525882", "−3.92910649036593", "8.53E-05"], ["RP11-21B23.2", "0.047448381", "1.048592072", "1.023032534", "1.074790193", 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