Identification of potential core genes in triple negative breast cancer using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30140156", "kind": "science-record", "revision": 8, "content_hash": "sha256:f625e7d419d762a15876c838cc8160bcacc6697cb378a3c584b8c9f40931534f", "created_at": "2026-11-01T15:40:36Z", "updated_at": "2026-11-01T22:00:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential core genes in triple negative breast cancer using bioinformatics analysis.", "doi": "10.2147/OTT.S166567", "pmid": "30140156", "authors": ["Man-Xiu Li", "Li-Ting Jin", "Tie-Jun Wang", "Yao-Jun Feng", "Cui-Ping Pan", "Dei-Mian Zhao", "Jun Shao"], "journal": "OncoTargets and therapy", "year": 2018, "abstract": "BACKGROUND: Triple-negative breast cancer (TNBC) is a subtype of breast cancer with poor clinical outcome and limited treatment options. Lacking molecular targets, chemotherapy is the main adjuvant treatment for TNBC patients.\nMATERIALS AND METHODS: To explore potential therapeutic targets for TNBC, we analyzed three microarray datasets (GSE38959, GSE45827, and GSE65194) derived from the Gene Expression Omnibus (GEO) database. The GEO2R tool was used to screen out differentially expressed genes (DEGs) between TNBC and normal tissue. Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed using the Database for Annotation, Visualization and Integrated Discovery to identify the pathways and functional annotation of DEGs. Protein-protein interaction of these DEGs was analyzed based on the Search Tool for the Retrieval of Interacting Genes database and visualized by Cytoscape software. In addition, we used the online Kaplan-Meier plotter survival analysis tool to evaluate the prognostic value of hub genes expression in breast cancer patients.\nRESULTS: A total of 278 upregulated DEGs and 173 downregulated DEGs were identified. Among them, ten hub genes with a high degree of connectivity were picked out. Overexpression of these hub genes was associated with unfavorable prognosis of breast cancer, especially, CCNB1 overexpression was observed and indicated poor outcome of TNBC.\nCONCLUSION: Our study suggests that CCNB1 was overexpressed in TNBC compared with normal breast tissue, and overexpression of CCNB1 was an unfavorable prognostic factor of TNBC patients. Further study is needed to explore the value of CCNB1 in the treatment of TNBC.", "claims": [{"id": "claim-method", "statement": "To investigate the prognostic values of the ten potential hub genes, the Kaplan–Meier plotter bioinformatics analysis platform was used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30140156", "locator": "sections[12] \"Survival analysis of ten hub genes\" paragraph 2", "quote": "To investigate the prognostic values of the ten potential hub genes, the Kaplan–Meier plotter bioinformatics analysis platform was used."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. Among them, GSE38959 contained 30 TNBC samples and 13 normal samples, and GSE45827 and GSE65194 included 41 TNBC specimens and eleven normal breast specimens respectively (Table 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30140156", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array)."}, {"asset": "source:pmid:30140156", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors."}, {"asset": "source:pmid:30140156", "locator": "sections[9] \"Identification of DEGs\" paragraph 2", "quote": "Among them, GSE38959 contained 30 TNBC samples and 13 normal samples, and GSE45827 and GSE65194 included 41 TNBC specimens and eleven normal breast specimens respectively (Table 1)."}], "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:30140156"], "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:GSE38959"], "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:GSE38959"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30140156", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S166567", "sha256": "sha256:f7f9837a18c047d6955936aca1effa02d5ce20d3f5ff4d245e27910adb85fef3", "bytes": 17391, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S166567", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6054764", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE38959", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38959", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38959", "version": null, "note": "Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. Among them, GSE38959 contained 30 TNBC samples and 13 normal samples, and GSE45827 and GSE65194 included 41 TNBC specimens and eleven normal breast specimens respectively (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. Among them, GSE38959 contained 30 TNBC samples and 13 normal samples, and GSE45827 and GSE65194 included 41 TNBC specimens and eleven normal breast specimens respectively (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM952871", "GSM952872", "GSM952873", "GSM952874", "GSM952875", "GSM952876", "GSM952877", "GSM952878", "GSM952879", "GSM952880", "GSM952881", "GSM952882", "GSM952883", "GSM952884", "GSM952885", "GSM952886", "GSM952887", "GSM952888", "GSM952889", "GSM952890", "GSM952891", "GSM952892", "GSM952893", "GSM952894", "GSM952895", "GSM952896", "GSM952897", "GSM952898", "GSM952899", "GSM952900", "GSM952901", "GSM952902", "GSM952903", "GSM952904", "GSM952905", "GSM952906", "GSM952907", "GSM952908", "GSM952909", "GSM952910", "GSM952911", "GSM952912", "GSM952913", "GSM952914", "GSM952915", "GSM952916", "GSM952917"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Gene expression profiling of triple negative breast cancer, normal ductal cells, and normal tissues", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE45827", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45827", "version": null, "note": "Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. Among them, GSE38959 contained 30 TNBC samples and 13 normal samples, and GSE45827 and GSE65194 included 41 TNBC specimens and eleven normal breast specimens respectively (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. 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All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. Among them, GSE38959 contained 30 TNBC samples and 13 normal samples, and GSE45827 and GSE65194 included 41 TNBC specimens and eleven normal breast specimens respectively (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. 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"capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE38959", "GSE45827", "GSE65194"], "resolved_accessions": ["GSE38959", "GSE45827", "GSE65194"], "statements": ["Among them, GSE38959 was based on the Agilent GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4×44K G4112F), and GSE45827 and GSE65194 were based on platform GPL570 ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). All of the data were freely available online, and this study did not involve any experiment on humans or animals performed by any of the authors. Among them, GSE38959 contained 30 TNBC samples and 13 normal samples, and GSE45827 and GSE65194 included 41 TNBC specimens and eleven normal breast specimens respectively (Table 1)."], "basis": "The paper names GSE38959, GSE45827, GSE65194 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:30140156", "data:geo:GSE38959", "asset:table:pmid:30140156:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE38959"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 13759, "completion_tokens": 2280, "cached_tokens": 4608}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30140156", "type": "paper", "label": "pmid:30140156"}, {"id": "source:pmid:30140156", "type": "manuscript", "label": "PMID 30140156 full text"}, {"id": "data:geo:GSE38959", "type": "dataset", "label": "GEO GSE38959"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30140156", "type": "paper", "label": "pmid:30140156"}, {"id": "source:pmid:30140156", "type": "manuscript", "label": "PMID 30140156 full text"}, {"id": "data:geo:GSE38959", "type": "dataset", "label": "GEO GSE38959"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30140156", "type": "extraction", "used": ["source:pmid:30140156"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE38959", "type": "accession_resolution", "used": ["data:geo:GSE38959"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:30140156", "parent_hash": "sha256:e343125999a6a7cea51196d5a2f89e84cc62d63c4307f42a4a229f730cef674d", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE38959 licence not read", "asset:data:geo:GSE38959 not downloaded", "asset:data:geo:GSE45827 licence not read", "asset:data:geo:GSE45827 not downloaded", "asset:data:geo:GSE65194 licence not read", "asset:data:geo:GSE65194 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["rapeutic targets for TNBC, we analyzed three microarray datasets (GSE38959, GSE45827, and GSE65194)"], "order_basis": "paper_text_order:377", "id": "assay:1"}, {"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:2"}]}