Unraveling breast cancer prognosis: a novel model based on coagulation-related genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38751445", "kind": "science-record", "revision": 3, "content_hash": "sha256:0f142ca97a27defdda1f53c473a41a4dd6a05c3844bbd71e6173d5db33449037", "created_at": "2026-11-01T19:20:42Z", "updated_at": "2026-11-01T22:11:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Unraveling breast cancer prognosis: a novel model based on coagulation-related genes.", "doi": "10.3389/fmolb.2024.1394585", "pmid": "38751445", "authors": ["Chuqi Lei", "Yuan Li", "Huaiyu Yang", "Ke Zhang", "Wei Lu", "Nianchang Wang", "Lixue Xuan"], "journal": "Frontiers in molecular biosciences", "year": 2024, "abstract": "Objective: Breast cancer is highly heterogeneous, presenting challenges in prognostic assessment. Developing a universally applicable prognostic model could simplify clinical decision-making. This study aims to develop and validate a novel breast cancer prognosis model using coagulation-related genes with broad clinical applicability.\nMethods: A total of 203 genes related to coagulation were obtained from the KEGG database, and the mRNA data of 1,099 tumor tissue samples and 572 samples of normal tissue were retrieved from the TCGA-BRCA cohort and GTEx databases. The R package \"limma\" was utilized to detect variations in gene expression related to coagulation between the malignancies and normal tissue. A model was constructed in the TCGA cohort through a multivariable Cox regression analysis, followed by validation using the GSE42568 dataset as the testing set. Constructing a nomogram incorporating clinical factors to enhance the predictive capacity of the model. Utilizing the ESTIMATE algorithm to investigate the immune infiltration levels in groups with deferent risk. Performing drug sensitivity analysis using the \"oncoPredict\" package.\nResults: A risk model consisting of six coagulation-associated genes (SERPINA1, SERPINF2, C1S, CFB, RASGRP1, and TLN2) was created and successfully tested for validation. Identified were 6 genes that serve as protective factors in the model's development. Kaplan-Meier curves revealed a worse prognosis in the high-risk group compared to the low-risk group. The ROC analysis showed that the model accurately forecasted the overall survival (OS) of breast cancer patients at 1, 3, and 5 years. Nomogram accompanied by calibration curves can also provide better guidance for clinical decision-making. The low-risk group is more likely to respond well to immunotherapy, whereas the high-risk group may show improved responses to Gemcitabine treatment. Furthermore, individuals in distinct risk categories displayed different responses to various medications within the identical therapeutic category.\nConclusion: We established a breast cancer prognostic model incorporating six coagulation-associated genes and explored its clinical utility. This model offers valuable insights for clinical decision-making and drug selection in breast cancer patients, contributing to personalized and precise treatment advancements.", "claims": [{"id": "claim-method", "statement": "With the aid of multivariate Cox regression analysis, a prognostic model was developed based on those prognostic related CRGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38751445", "locator": "sections[7] \"2.5 Development and validation of the prognostic model\" paragraph 2", "quote": "With the aid of multivariate Cox regression analysis, a prognostic model was developed based on those prognostic related CRGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38751445", "locator": "sections[24] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A six-gene breast cancer prognostic model was developed with multivariable Cox regression in the TCGA cohort and validated using GSE42568.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38751445", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "A model was constructed in the TCGA cohort through a multivariable Cox regression analysis, followed by validation using the GSE42568 dataset as the testing set."}, {"asset": "source:pmid:38751445", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A risk model consisting of six coagulation-associated genes (SERPINA1, SERPINF2, C1S, CFB, RASGRP1, and TLN2) was created and successfully tested for validation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A six-gene breast cancer prognostic model was developed with multivariable Cox regression in the TCGA cohort and validated using GSE42568.", "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:38751445"], "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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