Bioinformatics analysis of key genes in triple negative breast cancer and validation of oncogene PLK1.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33490149", "kind": "science-record", "revision": 9, "content_hash": "sha256:1ec8170005093f1241f75e19d56522f41b7de2b7370b64594eb9c169decaf535", "created_at": "2026-11-01T15:41:23Z", "updated_at": "2026-11-01T22:46:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of key genes in triple negative breast cancer and validation of oncogene PLK1.", "doi": "10.21037/atm-20-6873", "pmid": "33490149", "authors": ["Yi Ren", "Rong Deng", "Qian Zhang", "Jing Li", "Baosan Han", "Ping Ye"], "journal": "Annals of translational medicine", "year": 2020, "abstract": "BACKGROUND: Breast cancer is the most common malignancy in women. Triple-negative breast cancer (TNBC) refers to a special subtype that is deficient in the expression of estrogen (ER), progesterone (PR), and human epidermal growth factor receptor 2 (HER-2). In this study, a variety of bioinformatics analysis tools were used to screen Hub genes related to the occurrence and development of triple negative breast cancer, and their biological functions were analyzed.\nMETHODS: Gene Expression Omnibus (GEO) breast cancer microarray data GSE62931 was selected as the research object. The differentially expressed genes (DEGs) were screened and the protein-protein interaction (PPI) network of DEGs was constructed using bioinformatics tools. The Hub genes were also screened. The Gene Ontology (GO) knowledgebase and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for biological enrichment analysis. The Gene Expression Profiling Interactive Analysis (GEPIA) online tool was used to verify the expression of the screened genes and patient survival. The effects of polo-like kinase 1 (PLK1) on the proliferation, invasion, migration, and dryness of breast cancer cells were verified using cell counting kit 8 (CCK-8), transwell migration assays, scratch tests, and clone formation tests. An animal model of subcutaneous xenotransplantation of breast cancer was established to evaluate the effect of PLK1 on the proliferation of breast cancer.\nRESULTS: A total of 824 DEGs were screened by GSE62931 microarray data; 405 of which were up-regulated and 419 of which were down-regulated. Functional enrichment analysis showed that these DEGs were mainly enriched in cancer-related pathways and were primarily involved in biological processes (BP) such as cell and mitotic division. From the Hub gene screening, PLK1 was further identified as the Hub gene associated with TNBC. Cell and animal experiments indicated that PLK1 promotes the proliferation, invasion, migration, and clone formation of breast cancer cells.\nCONCLUSIONS: Gene chip combined with bioinformatics methods can effectively analyze the DEGs related to the occurrence and development of breast cancer, and the screening of PLK1 can provide theoretical guidance for further research on the molecular mechanism of breast cancer and the screening of molecular markers.", "claims": [{"id": "claim-method", "statement": "The statistical method used was the independent sample t-test. One-way analysis of variance (ANOVA) was used for comparison among groups. P<0.05 was considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33490149", "locator": "sections[18] \"Statistical analysis\" paragraph 2", "quote": "The statistical method used was the independent sample t-test. One-way analysis of variance (ANOVA) was used for comparison among groups. P<0.05 was considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this study, GEO breast cancer microarray data GSE62931 gene expression profile chip was selected as the research object (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62931), which was Affymetrix Human Genome U1332.0 chip [HGU133_Plus_2]u (Agilent GPL15048 platform). The GSE62931 data set consisted of 53 breast cancer tumor tissue chips and 53 TNBC tumor tissue chips.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33490149", "locator": "sections[3] \"GEO data downloads\" paragraph 2", "quote": "In this study, GEO breast cancer microarray data GSE62931 gene expression profile chip was selected as the research object (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62931), which was Affymetrix Human Genome U1332.0 chip [HGU133_Plus_2]u (Agilent GPL15048 platform). The GSE62931 data set consisted of 53 breast cancer tumor tissue chips and 53 TNBC tumor tissue chips."}], "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:33490149"], "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:GSE62931"], "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:GSE62931"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33490149", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-20-6873", "sha256": "sha256:2e6d60d474fa0fd1316b5989d4b7394be5e34c5357ce7872ada1dbddc30798af", "bytes": 34408, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-20-6873", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7812170", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62931", "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=GSE62931", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62931", "version": null, "note": "In this study, GEO breast cancer microarray data GSE62931 gene expression profile chip was selected as the research object (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62931), which was Affymetrix Human Genome U1332.0 chip [HGU133_Plus_2]u (Agilent GPL15048 platform). The GSE62931 data set consisted of 53 breast cancer tumor tissue chips and 53 TNBC tumor tissue chips.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In this study, GEO breast cancer microarray data GSE62931 gene expression profile chip was selected as the research object (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62931), which was Affymetrix Human Genome U1332.0 chip [HGU133_Plus_2]u (Agilent GPL15048 platform). The GSE62931 data set consisted of 53 breast cancer tumor tissue chips and 53 TNBC tumor tissue chips.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1536443", "GSM1536444", "GSM1536445", "GSM1536446", "GSM1536447", "GSM1536448", "GSM1536449", "GSM1536450", "GSM1536451", "GSM1536452", "GSM1536453", "GSM1536454", "GSM1536455", "GSM1536456", "GSM1536457", "GSM1536458", "GSM1536459", "GSM1536460", "GSM1536461", "GSM1536462", "GSM1536463", "GSM1536464", "GSM1536465", "GSM1536466", "GSM1536467", "GSM1536468", "GSM1536469", "GSM1536470", "GSM1536471", "GSM1536472", "GSM1536473", "GSM1536474", "GSM1536475", "GSM1536476", "GSM1536477", "GSM1536478", "GSM1536479", "GSM1536480", "GSM1536481", "GSM1536482", "GSM1536483", "GSM1536484", "GSM1536485", "GSM1536486", "GSM1536487", "GSM1536488", "GSM1536489", "GSM1536490", "GSM1536491", "GSM1536492", "GSM1536493", "GSM1536494", "GSM1536495", "GSM1536496", "GSM1536497", "GSM1536498", "GSM1536499", "GSM1536500", "GSM1536501", "GSM1536502", "GSM1536503", "GSM1536504", "GSM1536505", "GSM1536506", "GSM1536507", "GSM1536508", "GSM1536509", "GSM1536510", "GSM1536511", "GSM1536512", "GSM1536513", "GSM1536515", "GSM1536516", "GSM1536517", "GSM1536519", "GSM1536520", "GSM1536521", "GSM1536522", "GSM1536523", "GSM1536524", "GSM1536526", "GSM1536527", "GSM1536529", "GSM1536530", "GSM1536531", "GSM1536532", "GSM1536533", "GSM1536534", "GSM1536535", "GSM1536536", "GSM1536537", "GSM1536538", "GSM1536539", "GSM1536541", "GSM1536542", "GSM1536543", "GSM1536544", "GSM1536545", "GSM1536546", "GSM1536548"], "sample_count": 100, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "Baseline expression profiles of human breast carcinomas", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE62931 not downloaded", "asset:data:geo:GSE62931 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The statistical method used was the independent sample t-test. One-way analysis of variance (ANOVA) was used for comparison among groups. P<0.05 was considered statistically significant."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE62931"], "resolved_accessions": ["GSE62931"], "statements": ["In this study, GEO breast cancer microarray data GSE62931 gene expression profile chip was selected as the research object (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62931), which was Affymetrix Human Genome U1332.0 chip [HGU133_Plus_2]u (Agilent GPL15048 platform). The GSE62931 data set consisted of 53 breast cancer tumor tissue chips and 53 TNBC tumor tissue chips."], "basis": "The paper names GSE62931 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:33490149", "data:geo:GSE62931"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62931"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:21Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 25561, "completion_tokens": 1290, "cached_tokens": 792}}, "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:33490149", "type": "paper", "label": "pmid:33490149"}, {"id": "source:pmid:33490149", "type": "manuscript", "label": "PMID 33490149 full text"}, {"id": "data:geo:GSE62931", "type": "dataset", "label": "GEO GSE62931"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33490149", "type": "paper", "label": "pmid:33490149"}, {"id": "source:pmid:33490149", "type": "manuscript", "label": "PMID 33490149 full text"}, {"id": "data:geo:GSE62931", "type": "dataset", "label": "GEO GSE62931"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33490149", "type": "extraction", "used": ["source:pmid:33490149"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62931", "type": "accession_resolution", "used": ["data:geo:GSE62931"], "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:33490149", "parent_hash": "sha256:ed133ba5cb604fd98649a474f39699b7f7037154164bcfaeb918dc85bf6feab6", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE62931 licence not read", "asset:data:geo:GSE62931 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["lls were verified using cell counting kit 8 (CCK-8), transwell migration assays, scratch tests,"], "order_basis": "paper_text_order:1280", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["um was replaced as required. Cell lines were transfected with PLK1 small interfering ribonucleic acid", "ding to the manufacturer’s instructions. The transfected cells were used 48 h later. Statistical anal", "ith PLK1 small interfering ribonucleic acid (siRNA) (20 nM) and overexpressed plasmid. Lipofect", "lle, MA, USA) was used, and negative control siRNA (si-NC) and si-PLK1 were transferred into th"], "order_basis": "paper_text_order:2996", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The statistical method used was the independent sample t-test. One-way analysis of variance (ANOVA) was used for comparison among groups. P<0.05 was considered statistically significant."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}