Assessing the prognostic value of stemness-related genes in breast cancer patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33110086", "kind": "science-record", "revision": 7, "content_hash": "sha256:5b663c42fe7f9465ffa69c2ee85a070a51f828b40c5937d25afb563c8dd97837", "created_at": "2026-11-01T15:41:14Z", "updated_at": "2026-11-01T22:02:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Assessing the prognostic value of stemness-related genes in breast cancer patients.", "doi": "10.1038/s41598-020-73164-3", "pmid": "33110086", "authors": ["Wen-Jie Wang", "Han Wang", "Meng-Sen Wang", "Yue-Qing Huang", "Yu-Yuan Ma", "Jie Qi", "Jian-Ping Shi", "Wei Li"], "journal": "Scientific reports", "year": 2020, "abstract": "Breast cancer (BC) is currently one of the deadliest tumors worldwide. Cancer stem cells (CSCs) are a small group of tumor cells with self-renewal and differentiation abilities and high treatment resistance. One of the reasons for treatment failures is the inability to completely eliminate tumor stem cells. By using the edgeR package, we identified stemness-related differentially expressed genes in GSE69280. Via Lasso-penalized Cox regression analysis and univariate Cox regression analysis, survival genes were screened out to construct a prognostic model. Via nomograms and ROC curves, we verified the accuracy of the prognostic model. We selected 4 genes (PSMB9, CXCL13, NPR3, and CDKN2C) to establish a prognostic model from TCGA data and a validation model from GSE24450 data. We found that the low-risk score group had better OS than the high-risk score group, whether using TCGA or GSE24450 data. A prognostic model including four stemness-related genes was constructed in our study to determine targets of breast cancer stem cells (BCSCs) and improve the treatment effect.", "claims": [{"id": "claim-method", "statement": "Patient survival time was analyzed using the KM curve, and the log-rank test was used for statistical analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33110086", "locator": "sections[17] \"Statistical analysis\" paragraph 2", "quote": "Patient survival time was analyzed using the KM curve, and the log-rank test was used for statistical analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analyzed during the current study are available in the TCGA and GEO repositories.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33110086", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "The datasets generated and analyzed during the current study are available in the TCGA and GEO repositories."}], "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:33110086"], "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:GSE24450"], "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:GSE24450"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33110086", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-020-73164-3", "sha256": 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{"label": "Table 1", "caption": "The clinical features of TCGA breast cancer patients.", "rows": [["Clinical features"], ["Age (years)", "Media", "58"], ["", "Rage", "26–89"], ["", "Numbers of patients (n = 1066)", "Numbers of patients (%)"], ["Gender", "Female", "1055 (98.97)"], ["Male", "11 (1.03)"], ["T stage", "T1", "280 (26.27)"], ["T2", "617 (57.88)"], ["T3", "131 (12.29)"], ["T4", "36 (3.38)"], ["Unknown", "2 (0.18)"], ["N stage", "0", "501 (47.00)"], ["1", "358 (33.58)"], ["2", "118 (11.69)"], ["3", "74 (6.94)"], ["Unknown", "15 (0.79)"], ["M stage", "0", "888 (83.80)"], ["1", "19 (1.78)"], ["Unknown", "159 (14.42)"], ["AJCC stage", "I", "183 (17.17)"], ["II", "602 (56.47)"], ["III", "240 (22.51)"], ["IV", "19 (1.78)"], ["Unknown", "20 (2.07)"], ["HER-2 status", "Positive", "156 (14.63)"], ["Negative", "560 (52.53)"], ["Unknown", "350 (32.84)"], ["Estrogen receptor status", "Positive", "787 (73.83)"], ["Negative", "233 (21.86)"], ["Unknown", "46 (4.31)"]], "row_count": 30, 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