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pmid:24809982
A long non-coding RNA signature to improve prognosis prediction of colorectal cancer.
Ye Hu · Hao-Yan Chen · Chen-Yang Yu · Jie Xu · Ji-Lin Wang · Jin Qian · Xi Zhang · Jing-Yuan Fang
Oncotarget · 2014 doi:10.18632/oncotarget.1895
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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We aimed to develop a lncRNA signature to improve prognosis prediction of colorectal cancer (CRC). Using a lncRNA-mining approach, we performed lncRNA expression profiling in large CRC cohorts from Gene Expression Ominus (GEO), including GSE39582 test series(N=436), internal validation series (N=117); and two independent validation series GSE14333 (N=197) and GSE17536(N=145). We established a set of six lncRNAs that were significantly correlated with the disease free survival (DFS) in the test series. Based on this six-lncRNA signature, the test series patients could be classified into high-risk and low-risk subgroups with significantly different DFS (HR=2.670; P<0.0001). The prognostic value of this six-lncRNA signature was confirmed in the internal validation series and another two independent CRC sets. Gene set enrichment analysis (GSEA) analysis suggested that risk score positively correlated with several cancer metastasis related pathways. Functional experiments demonstrated three dysregulated lncRNAs, AK123657, BX648207 and BX649059 were required for efficient invasion and proliferation suppression in CRC cell lines. Our results might provide an efficient classification tool for clinical prognosis evaluation of CRC.", "claims": [{"id": "claim-method", "statement": "The association between the lncRNA expression and patient's disease free survival (DFS) and disease specific survival (DSS) was assessed by univariable Cox regression analysis along with a permutation test using Biometric Research Branch-Array (BRB-Array) Tools [39].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24809982", "locator": "sections[15] \"Statistical analysis\" paragraph 2", "quote": "The association between the lncRNA expression and patient's disease free survival (DFS) and disease specific survival (DSS) was assessed by univariable Cox regression analysis along with a permutation test using Biometric Research Branch-Array (BRB-Array) Tools [39]."}], "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 GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24809982", "locator": "sections[24] \"Data sharing statement\" paragraph 2", "quote": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used univariable and multivariable Cox proportional hazards regression, Kaplan–Meier analysis with log-rank tests, and GSEA; source microarray data and clinical data were obtained from the public GEO database, with prognostic lncRNAs selected in the GSE39582 test series and validated in internal and independent cohorts. 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"1.99E-04", "1.379", "0.24326"]], "row_count": 7, "column_count": 4, "numeric_cells": 24, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:24809982:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:19c2d4e889bc79b6af350bcb0f918e09adc684c7686f633b6601281cecd88225", "bytes": 3268, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T2", "version": null, "note": "Univariable and multivariable Cox regression analysis in each data set", "structure": {"pmcid": "PMC4039159", "section_index": 5, "section_title": "The six-lncRNA signature and patients' survival in the test series", "row_count": 46, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariable and multivariable Cox regression analysis in each data set", "rows": [["Variables", "Univariable modela", "Multivariable modela"], ["", "HR", "95% CI of HR", "P value", "HR", "95% CI of HR", "P value"], ["GSE39582 test series(N=436)", "", "", "", "", ""], ["Six-lncRNA risk score", "2.717", "2.005 to 3.682", "<0.0001", "2.353", "1.723 to 3.214", "<0.0001"], ["Age", "1", "0.988 to 1.012", "0.9588", "1.005", "0.992 to 1.018", "0.4308"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "5.749", "0.793 to 41.661", "0.0835", "4.051", "0.557to 29.452", "0.1669"], ["3", "9.263", "1.284 to 66.828", "0.0273", "6.07", "0.837 to 44.028", "0.0745"], ["4", "31.434", "4.281 to 230.822", "0.0007", "20.837", "2.813 to 154.324", "0.003"], ["Gender", "1.337", "0.955 to 1.871", "0.0911", "1.585", "1.126 to 2.232", "0.0082"], ["GSE39582 valiation series(N=117)", "", "", "", "", ""], ["Six-lncRNA risk score", "2.271", "1.424 to 3.622", "0.0006", "2.095", "1.190 to 3.688", "0.0103"], ["Age", "1.000", "0.973 to 1.028", "0.9815", "1.02", "0.987 to 1.054", "0.2458"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "2674096", "0.000 to", "0.9906", "1994681", "0.000 to", "0.9916"], ["3", "9681475", "0.000 to", "0.9898", "6897474", "0.000 to", "0.9909"], ["4", "1.57E+08", "0.000 to", "0.9880", "1.52E+00", "0.000 to", "0.9891"], ["Gender", "1.060", "0.543 to 2.073", "0.8639", "1.456", "0.711 to 2.983", "0.3044"], ["Entire GSE39582 set(N=553)", "", "", "", "", ""], ["Six-lncRNA risk score", "2.565", "1.992 to 3.302", "<0.0001", "2.221", "1.703 to 2.896", "<0.0001"], ["Age", "1.000", "0.989 to 1.011", "0.9544", "1.007", "0.995 to 1.019", "0.2574"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "7.717", "1.069 to 55.692", "0.0427", "5.203", "0.718 to 37.701", "0.1026"], ["3", "14.808", "2.061 to 106.413", "0.0074", "9.431", "1.305 to 68.148", "0.0262"], ["4", "52.841", "7.232 to 386.063", "<0.0001", "33.045", "4.621to 250.808", "0.0005"], ["Gender", "1.271", "0.941 to 1.717", "0.1177", "1.534", "1.130 to 2.083", "0.0061"], ["GSE14333 set(N=197)", "", "", "", "", ""], ["Six-lncRNA risk score", "3.229", "1.814 to 5.749", "<0.0001", "2.589", "1.411 to 4.752", "0.0021"], ["Age", "0.978", "0.957 to 1", "0.9544", "0.991", "0.968 to 1.015", "0.4679"], ["Duke stageb", "", "", "", "", "", ""], ["A", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["B", "2.927", "0.665 to 12.889", "0.1555", "2.533", "0.574 to 11.184", "0.2200"], ["C", "6.897", "1.639 to 29.025", "0.0084", "5.204", "1.223 to 22.147", "0.0256"], ["Gender", "1.118", "0.612 to 2.042", "0.7171", "0.997", "0.533 to 1.868", "0.9935"], ["GSE17536 set(N=145)", "", "", "", "", ""], ["Six-lncRNA risk score", "3.25", "1.658 to 6.368", "0.0006", "2.892", "1.407 to 5.944", "0.0039"], ["Age", "0.984", "0.961 to 1.007", "0.1595", "0.996", "0.970 to 1.022", "0.7465"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "5.382", "0.695 to 41.708", "0.1071", "4.66", "0.591 to 36.756", "0.1422"], ["3", "10.645", "1.428 to 79.327", "0.021", "8.445", "1.109 to 64.275", "0.0394"], ["4", "14.655", "1.637 to 131.184", "0.0164", "14.329", "1.572 to 130.581", "0.0184"], ["Gender", "1", "0.520 to 1.925", "1", "0.986", "0.482 to 2.019", "0.9703"]], "row_count": 46, "column_count": 7, "numeric_cells": 207, "header_rows": 2, "locator": "section[5]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE40966 not downloaded", "asset:data:geo:GSE40966 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": 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A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "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 catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:24809982", "data:geo:GSE14333", "asset:table:pmid:24809982:1", "asset:table:pmid:24809982:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14333"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:16Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 95963, "completion_tokens": 4938, "cached_tokens": 72522}}, "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:24809982", "type": "paper", "label": "pmid:24809982"}, {"id": "source:pmid:24809982", "type": "manuscript", "label": "PMID 24809982 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:24809982", "type": "paper", "label": "pmid:24809982"}, {"id": "source:pmid:24809982", "type": "manuscript", "label": "PMID 24809982 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-24809982", "type": "extraction", "used": ["source:pmid:24809982"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14333", "type": "accession_resolution", "used": ["data:geo:GSE14333"], "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:24809982", "parent_hash": "sha256:136b03618518539de5c053bce278902cd496773adc144e3a5aa9a1fffd526e3c", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE40966 licence not read", "asset:data:geo:GSE40966 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lysis in each data set MATERIALS AND METHODS Microarray data processing and lncRNA profile mining Th", "A customized R scripts was used to perform a microarray expression calculation according to the re-m"], "order_basis": "paper_text_order:3812", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["o a database for non-coding RNA of human and mouse derived from RNAdb [37]. 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