Identification of hub genes in triple-negative breast cancer by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33708561", "kind": "science-record", "revision": 5, "content_hash": "sha256:42149dcb513e360267888133eeaea3c19cc22df63f6820865a6294512e79c2be", "created_at": "2026-11-01T17:34:53Z", "updated_at": "2026-11-01T22:46:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes in triple-negative breast cancer by integrated bioinformatics analysis.", "doi": "10.21037/gs-21-17", "pmid": "33708561", "authors": ["Li-Min Wei", "Xin-Yang Li", "Zi-Ming Wang", "Yu-Kun Wang", "Ge Yao", "Jia-Hao Fan", "Xin-Shuai Wang"], "journal": "Gland surgery", "year": 2021, "abstract": "BACKGROUND: Triple negative breast cancer (TNBC) is usually aggressive and accompanied by a poor prognosis. The molecular biological mechanism of TNBC pathogenesis is still unclear, and requires more detailed research. The aim of this study was to screen and verify potential biomarkers of TNBC, and provide new clues for the treatment and diagnosis of TNBC.\nMETHODS: In this work, GSE76250 was downloaded from the Gene Expression Omnibus (GEO) database and included 165 TNBC samples and 33 paired normal breast tissues. The R software and its related software package were used for data processing and analysis. Compared with normal tissues, genes with a false discovery rate (FDR) <0.01 and log fold change (logFC) ≥1 or ≤-1 were identified as differentially expressed genes (DEGs) by limma package. Survival prognoses were analyzed by Kaplan-Meier plotter database.\nRESULTS: In total, 160 up-regulated and 180 down-regulated genes were identified. The biological mechanism of enrichment analysis presented that DEGs were significantly enriched in chromosome segregation, extracellular matrix, and extracellular matrix structural constituent, among others. A total of 8 hub genes (CCNB1, CDK1, TOP2A, MKI67, TTK, CCNA2, BUB1, and PLK1) were identified by the protein-protein interaction network (PPIN) and Cytoscape software. Survival prognosis of these hub genes showed that they were negatively correlated with overall survival.\nCONCLUSIONS: The 8 hub genes and pathways that were identified might be involved in tumorigenesis and become new candidate biomarkers for TNBC treatment.", "claims": [{"id": "claim-method", "statement": "Compared with normal tissues, genes with a false discovery rate (FDR) <0.01 and log fold change (logFC) ≥1 or ≤−1 were identified as differentially expressed genes (DEGs) by limma package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33708561", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Compared with normal tissues, genes with a false discovery rate (FDR) <0.01 and log fold change (logFC) ≥1 or ≤−1 were identified as differentially expressed genes (DEGs) by limma package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this work, GSE76250 was downloaded from the Gene Expression Omnibus (GEO) database and included 165 TNBC samples and 33 paired normal breast tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33708561", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In this work, GSE76250 was downloaded from the Gene Expression Omnibus (GEO) database and included 165 TNBC samples and 33 paired normal breast tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The 8 hub genes and pathways that were identified might be involved in tumorigenesis and become new candidate biomarkers for TNBC treatment.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33708561", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The 8 hub genes and pathways that were identified might be involved in tumorigenesis and become new candidate biomarkers for TNBC treatment."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The 8 hub genes and pathways that were identified might be involved in tumorigenesis and become new candidate biomarkers for TNBC treatment.", "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:33708561"], "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:GSE76250"], "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:GSE76250"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33708561", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/gs-21-17", "sha256": 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