A four-long non-coding RNA signature in predicting breast cancer survival.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25288503", "kind": "science-record", "revision": 7, "content_hash": "sha256:80bd84dc0a42ff01f1d205aae89130d5199ed52c1eed241a5bafac3654c00486", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:19:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A four-long non-coding RNA signature in predicting breast cancer survival.", "doi": "10.1186/s13046-014-0084-7", "pmid": "25288503", "authors": ["Jin Meng", "Ping Li", "Qing Zhang", "Zhangru Yang", "Shen Fu"], "journal": "Journal of experimental & clinical cancer research : CR", "year": 2014, "abstract": "BACKGROUND: Many long non-coding RNAs(lncRNAs) have been found to be a good marker for several tumors. Using lncRNA-mining approach, we aimed to identify lncRNA expression signature that can predict breast cancer patient survival.\nMETHODS: We performed LncRNA expression profiling in 887 breast cancer patients from Gene Expression Omnibus (GEO) datasets. The association between lncRNA signature and clinical survival was analyzed using the training set(n = 327, from GSE 20685). The validation for the association was performed in another three independent testing sets(252 from GSE21653, 204 from GSE12276, and 104 from GSE42568).\nRESULTS: A set of four lncRNA genes (U79277, AK024118, BC040204, AK000974) have been identified by the random survival forest algorithm. Using a risk score based on the expression signature of these lncRNAs, we separated the patients into low-risk and high-risk groups with significantly different survival times in the training set. This signature was validated in the other three cohorts. Further study revealed that the four-lncRNA expression signature was independent of age and subtype. Gene Set Enrichment Analysis (GSEA) suggested that gene sets were involved in several cancer metastasis related pathways.\nCONCLUSIONS: These findings indicate that lncRNAs may be implicated in breast cancer pathogenesis. The four-lncRNA signature may have clinical implications in the selection of high-risk patients for adjuvant therapy.", "claims": [{"id": "claim-method", "statement": "Considering that a smaller number of genes in the model would make the model more practical, we then performed the random survival forests-variable hunting (RSFVH) algorithm [39].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25288503", "locator": "sections[6] \"Statistical analysis\" paragraph 2", "quote": "Considering that a smaller number of genes in the model would make the model more practical, we then performed the random survival forests-variable hunting (RSFVH) algorithm [39]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Breast cancer gene expression data and corresponding clinical data used in this study were obtained from the publicly available GEO databases. We followed the strategy of using the largest data set (GSE20685) as training set. After filtering out samples without clinical survival information, there were a total of 887 samples, including 327 from GSE20685, 252 from GSE21653, 204 from GSE12276, and 104 from GSE42568, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25288503", "locator": "sections[3] \"GEO breast cancer gene expression data\" paragraph 2", "quote": "Breast cancer gene expression data and corresponding clinical data used in this study were obtained from the publicly available GEO databases."}, {"asset": "source:pmid:25288503", "locator": "sections[3] \"GEO breast cancer gene expression data\" paragraph 2", "quote": "We followed the strategy of using the largest data set (GSE20685) as training set."}, {"asset": "source:pmid:25288503", "locator": "sections[3] \"GEO breast cancer gene expression data\" paragraph 2", "quote": "After filtering out samples without clinical survival information, there were a total of 887 samples, including 327 from GSE20685, 252 from GSE21653, 204 from GSE12276, and 104 from GSE42568, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using breast-cancer microarray data obtained from GEO and re-annotated for lncRNA expression, the study applied univariable Cox regression and random survival forests to identify and validate a four-lncRNA survival signature (U79277, AK024118, BC040204, and AK000974).", "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:25288503"], "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. 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121, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Breast Cancer Gene Expression Analysis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:25288503:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b706d690919da1bfb51474e989622b0d8d9b0f2dbc45e3730d2280961f6e49dd", "bytes": 735, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#Tab1", "version": null, "note": "Four LncRNAs significantly associated with the overall survival in the training-set patients (n = 327)", "structure": {"pmcid": "PMC4198622", "section_index": 8, "section_title": "Identification of lncRNA genes from the training set", "row_count": 5, "column_count": 7}, "table": {"label": "Table 1", "caption": "Four LncRNAs significantly associated with the overall survival in the training-set patients (n = 327)", "rows": [["Gene symbol", "Chromosomal position", "Parametric P value", "Hazard ratio", "Coefficient", "Variable importance", "Relative importance"], ["AK024118", "chr18:59125236-59125296", "7.00E-07", "0.579", "−0.35717", "0.0369", "1.0000"], ["BC040204", "chr6:72153349-72153409", "1.93E-05", "0.428", "−0.48664", "0.0198", "0.5368"], ["AK000974", "chr10:97810995-97811055", "2.85E-05", "0.416", "−0.48122", "0.0173", "0.4683"], ["U79277", "chr8:101998264-101998324", "4.30E-06", "2.17", "0.518242", "0.0200", "0.5411"]], "row_count": 5, "column_count": 7, "numeric_cells": 28, "header_rows": 1, "locator": "section[8]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:25288503:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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