Identification of key biomarkers in breast cancer based on bioinformatics analysis and experimental verification.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39988630", "kind": "science-record", "revision": 3, "content_hash": "sha256:2c49d3b7328d5ffc01285dee6ac4339f4cf5e030a678e520a0e28fad26ac697f", "created_at": "2026-11-01T20:30:13Z", "updated_at": "2026-11-01T22:13:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key biomarkers in breast cancer based on bioinformatics analysis and experimental verification.", "doi": "10.1186/s43046-025-00260-8", "pmid": "39988630", "authors": ["Yu Huan", "Ping She", "Xushan Cai", "Jiehua Qi", "Chunli Zhang"], "journal": "Journal of the Egyptian National Cancer Institute", "year": 2025, "abstract": "BACKGROUND: Breast cancer (BC) is a malignant tumor characterized by a high incidence rate and is the leading cause of cancer-related deaths among women worldwide. This study aims to identify key genes and potential prognostic biomarkers using a bioinformatics approach.\nMETHODS: Three microarray datasets, GSE86374, GSE120129, and GSE29044, were downloaded from the GEO database. GEO2R and Venn diagram software were employed to identify differentially expressed genes (DEGs), while DAVID was utilized for functional enrichment analysis. Subsequently, STRING and Cytoscape were used to construct the protein-protein interaction (PPI) network among the DEGs. UALCAN, GEPIA, and the Kaplan-Meier plotter were employed for prognostic analysis. Following this, the correlations and alterations of key genes were examined using cBioPortal. Finally, immunohistochemistry (IHC) was performed to validate the expression levels of the key genes.\nRESULTS: A total of 323 differentially expressed genes (DEGs) were identified. From the protein-protein interaction (PPI) network, 37 hub genes were selected. Validation using UALCAN, GEPIA, and Kaplan-Meier plotters revealed that three key genes-RACGAP1, SPAG5, and KIF20A-were significantly overexpressed and associated with poor prognosis in breast cancer (BC), as well as advanced tumor staging. The correlations and alterations of these key genes, as demonstrated on cBioPortal, indicated that their alterations co-occurred. Experimental verification through immunohistochemistry (IHC) confirmed that the proteins of these key genes were highly expressed in tumor tissues.\nCONCLUSIONS: The key genes identified in this study can enhance our understanding of the molecular mechanisms underlying breast cancer (BC). Additionally, these genes may serve as potential sensitive biomarkers for patients with BC.", "claims": [{"id": "claim-method", "statement": "DEGs between tumor and normal tissue in the breast of the three databases above were made out by GEO2R. The criteria for identifying DEGs were based on LogFC (fold change) ≥ 1 or LogFC ≤ − 1, and P-value < 0.05 were deemed to be statistically significant. Whereupon, the general DEGs in the three separate cohorts were picked out by Venn (http://bioinformatics.psb.ugent.be/webtools/Venn/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39988630", "locator": "sections[4] \"Classification of DEGs\" paragraph 2", "quote": "DEGs between tumor and normal tissue in the breast of the three databases above were made out by GEO2R. The criteria for identifying DEGs were based on LogFC (fold change) ≥ 1 or LogFC ≤ − 1, and P-value < 0.05 were deemed to be statistically significant. Whereupon, the general DEGs in the three separate cohorts were picked out by Venn (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GEO (http://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39988630", "locator": "sections[25] \"Data availability\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GEO (http://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified RACGAP1, SPAG5, and KIF20A as significantly overexpressed key genes associated with poor prognosis and advanced tumor staging in breast cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39988630", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Validation using UALCAN, GEPIA, and Kaplan–Meier plotters revealed that three key genes—RACGAP1, SPAG5, and KIF20A—were significantly overexpressed and associated with poor prognosis in breast cancer (BC), as well as advanced tumor staging."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified RACGAP1, SPAG5, and KIF20A as significantly overexpressed key genes associated with poor prognosis and advanced tumor staging in breast cancer.", "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:39988630"], "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:GSE120129"], "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:GSE120129"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39988630", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s43046-025-00260-8", "sha256": 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The criteria for identifying DEGs were based on LogFC (fold change) ≥ 1 or LogFC ≤ − 1, and P-value < 0.05 were deemed to be statistically significant. Whereupon, the general DEGs in the three separate cohorts were picked out by Venn (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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METHODS: Three microarray datasets, GSE86374, GSE120129, and GSE29044,"], "order_basis": "paper_text_order:355", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nes were examined using cBioPortal. Finally, immunohistochemistry (IHC) was performed to validate the expressi", "-occurred. Experimental verification through immunohistochemistry (IHC) confirmed that the proteins of these k", "g cBioPortal. Finally, immunohistochemistry (IHC) was performed to validate the expression le", "l verification through immunohistochemistry (IHC) confirmed that the proteins of these key ge"], "order_basis": "paper_text_order:914", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}