Identification of five hub genes as monitoring biomarkers for breast cancer metastasis in silico.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31285741", "kind": "science-record", "revision": 8, "content_hash": "sha256:9e52bef7c0a2a611f631e84a7d0c9a77d4f34584bc2988785890ffbb831993ea", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T22:44:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of five hub genes as monitoring biomarkers for breast cancer metastasis in silico.", "doi": "10.1186/s41065-019-0096-6", "pmid": "31285741", "authors": ["Yun Cai", "Jie Mei", "Zhuang Xiao", "Bujie Xu", "Xiaozheng Jiang", "Yongjie Zhang", "Yichao Zhu"], "journal": "Hereditas", "year": 2019, "abstract": "BACKGROUND: Breast cancer is one of the most common endocrine cancers among females worldwide. Distant metastasis of breast cancer is causing an increasing number of breast cancer-related deaths. However, the potential mechanisms of metastasis and candidate biomarkers remain to be further explored.\nRESULTS: The gene expression profiles of GSE102484 were downloaded from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was used to screen for the most potent gene modules associated with the metastatic risk of breast cancer, and a total of 12 modules were identified based on the analysis. In the most significant module (R2 = 0.68), 21 network hub genes (MM > 0.90) were retained for further analyses. Next, protein-protein interaction (PPI) networks were used to further explore the biomarkers with the most interactions in gene modules. According to the PPI networks, five hub genes (TPX2, KIF2C, CDCA8, BUB1B, and CCNA2) were identified as key genes associated with breast cancer progression. Furthermore, the prognostic value and differential expression of these genes were validated based on data from The Cancer Genome Atlas (TCGA) and Kaplan-Meier (KM) Plotter. Receiver operating characteristic (ROC) curve analysis revealed that the mRNA expression levels of these five hub genes showed excellent diagnostic value for breast cancer and adjacent tissues. Moreover, these five hub genes were significantly associated with worse distant metastasis-free survival (DMFS) in the patient cohort based on KM Plotter.\nCONCLUSION: Five hub genes (TPX2, KIF2C, CDCA8, BUB1B, and CCNA2) associated with the risk of distant metastasis were extracted for further research, which might be used as biomarkers to predict distant metastasis of breast cancer.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier survival plots were generated with survival curves compared by the log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31285741", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Kaplan-Meier survival plots were generated with survival curves compared by the log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data are included in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31285741", "locator": "sections[17] \"ack\" paragraph 1", "quote": "All data are included in the article."}], "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:31285741"], "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:GSE102484"], "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:GSE102484"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31285741", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s41065-019-0096-6", "sha256": 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