Identification of potential key genes for HER-2 positive breast cancer based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31895772", "kind": "science-record", "revision": 8, "content_hash": "sha256:8fdf44519cee8c5eff5d32c87c454939c37be3fb37ae7fe66f6fad3784a6d0e6", "created_at": "2026-11-01T15:40:54Z", "updated_at": "2026-11-01T22:01:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential key genes for HER-2 positive breast cancer based on bioinformatics analysis.", "doi": "10.1097/MD.0000000000018445", "pmid": "31895772", "authors": ["Yuxiang Lin", "Fangmeng Fu", "Jinxing Lv", "Mengchi Wang", "Yan Li", "Jie Zhang", "Chuan Wang"], "journal": "Medicine", "year": 2020, "abstract": "BACKGROUNDS: HER-2 positive breast cancer is a subtype of breast cancer with poor clinical outcome. The aim of this study was to identify differentially expressed genes (DEGs) for HER-2 positive breast cancer and elucidate the potential interactions among them.\nMATERIAL AND METHODS: Three gene expression profiles (GSE29431, GSE45827, and GSE65194) were derived from the Gene Expression Omnibus (GEO) database. GEO2R tool was applied to obtain DEGs between HER-2 positive breast cancer and normal breast tissues. Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery (David) online tool. Protein-protein interaction (PPI) network, hub gene identification and module analysis was conducted by Cytoscape software. Online Kaplan-Meier plotter survival analysis tool was also used to investigate the prognostic values of hub genes in HER-2 positive breast cancer patients.\nRESULTS: A total of 54 upregulated DEGs and 269 downregulated DEGs were identified. Among them, 10 hub genes including CCNB1, RAC1, TOP2A, KIF20A, RRM2, ASPM, NUSAP1, BIRC5, BUB1B, and CEP55 demonstrated by connectivity degree in the PPI network were screened out. In Kaplan-Meier plotter survival analysis, the overexpression of RAC1 and RRM2 were shown to be associated with an unfavorable prognosis in HER-2 positive breast cancer patients.\nCONCLUSIONS: This present study identified a number of potential target genes and pathways which might impact the oncogenesis and progression of HER-2 positive breast cancer. These findings could provide new insights into the detection of novel diagnostic and therapeutic biomarkers for this disease.", "claims": [{"id": "claim-method", "statement": "To investigate the prognostic values of hub genes in HER-2 positive breast cancer patients, the Kaplan–Meier plotter mRNA breast cancer database (http://kmplot.com/analysis/)[23] was performed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31895772", "locator": "sections[7] \"Survival analysis of hub genes\" paragraph 2", "quote": "To investigate the prognostic values of hub genes in HER-2 positive breast cancer patients, the Kaplan–Meier plotter mRNA breast cancer database (http://kmplot.com/analysis/)[23] was performed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Among them, the GSE29431 dataset includes 28 HER-2 positive breast cancer samples and 12 normal tissues samples, while the GSE45827 and GSE65194 expression profiles were from the same specimens and consist of 30 HER-2 positive breast cancer samples and 11 matched normal breast tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31895772", "locator": "sections[3] \"Datasets\" paragraph 2", "quote": "Among them, the GSE29431 dataset includes 28 HER-2 positive breast cancer samples and 12 normal tissues samples, while the GSE45827 and GSE65194 expression profiles were from the same specimens and consist of 30 HER-2 positive breast cancer samples and 11 matched normal breast tissues."}], "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:31895772"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:31895772", "data:geo:GSE29431", "asset:table:pmid:31895772:1", "asset:table:pmid:31895772:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29431"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 26716, "completion_tokens": 1938, "cached_tokens": 784}}, "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:31895772", "type": "paper", "label": "pmid:31895772"}, {"id": "source:pmid:31895772", "type": "manuscript", "label": "PMID 31895772 full text"}, {"id": "data:geo:GSE29431", "type": "dataset", "label": "GEO GSE29431"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31895772", "type": "paper", "label": "pmid:31895772"}, {"id": "source:pmid:31895772", "type": "manuscript", "label": "PMID 31895772 full text"}, {"id": "data:geo:GSE29431", "type": "dataset", "label": "GEO GSE29431"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31895772", "type": "extraction", "used": ["source:pmid:31895772"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29431", "type": "accession_resolution", "used": ["data:geo:GSE29431"], "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:31895772", "parent_hash": "sha256:245a6e66ddac395310f9188ad055da297d6ec72072d15d69ed095344729d6686", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE29431 licence not read", "asset:data:geo:GSE29431 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": ["across different groups of samples. The raw microarray data files between HER-2 positive breast can"], "order_basis": "paper_text_order:2028", "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"}]}