Biomarkers and potential function analysis of triple-negative breast cancer screening based on bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40179432", "kind": "science-record", "revision": 2, "content_hash": "sha256:db21065868df63c2c5a2f45d5005671e9f38641db3345edb45ffe8969a1e04e0", "created_at": "2026-11-01T20:30:22Z", "updated_at": "2026-11-01T21:34:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Biomarkers and potential function analysis of triple-negative breast cancer screening based on bioinformatics.", "doi": "10.1177/18758592241308738", "pmid": "40179432", "authors": ["Xing Chen", "Xiaodan Tan", "Zhe Peng", "Xiaoli Wang", "Wenjia Guo", "Dan Li", "Yang Yang", "Duanfang Zhou", "Lin Chen"], "journal": "Cancer biomarkers : section A of Disease markers", "year": 2025, "abstract": "This study aims to identify and validate potential endogenous biomarkers for triple-negative breast cancer (TNBC). TNBC microarray data (GSE38959, GSE53752) were retrieved from the Gene Expression Omnibus (GEO) database, and principal component analysis (PCA) was performed to evaluate the reliability of the data. The microarray datasets were merged, and differentially expressed genes (DEGs) were identified using R software. Functional enrichment analysis of the DEGs was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The most disease-relevant module was identified through Weighted Gene Co-expression Network Analysis (WGCNA), and genes within this module were intersected with the DEGs. The intersecting genes underwent Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis to minimize errors and identify TNBC-specific genes. Sensitivity and survival analyses were performed on the identified specific genes. There were 10 TNBC-specific genes identified: RRM2, DEPDC1, FIGF, TACC3, E2F1, CDO1, DST, MCM4, CHEK1, and PLSCR4. RT-qPCR analysis showed significant upregulation of CDO1, MCM4, DEPDC1, RRM2, and E2F1 in MDA-MB-231, CAL-148, and MFM-223 compared to MCF-10A. Our findings provide new insights into TNBC pathogenesis and potential therapeutic strategies, with important clinical implications for further understanding TNBC mechanisms and developing innovative treatments.", "claims": [{"id": "claim-method", "statement": "The intersecting genes underwent Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis to minimize errors and identify TNBC-specific genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40179432", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The intersecting genes underwent Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis to minimize errors and identify TNBC-specific genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE38959 comprises 30 surgically resected TNBC tissues and 13 normal mammary ductal cells, while GSE53752 consists of 51 TNBC tissues and 25 normal breast tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40179432", "locator": "sections[13] \"Identification of DEGs from GEO\" paragraph 2", "quote": "GSE38959 comprises 30 surgically resected TNBC tissues and 13 normal mammary ductal cells, while GSE53752 consists of 51 TNBC tissues and 25 normal breast tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO microarray data from GSE38959 and GSE53752, LASSO regression analysis identified 10 TNBC-specific genes: RRM2, DEPDC1, FIGF, TACC3, E2F1, CDO1, DST, MCM4, CHEK1, and PLSCR4.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40179432", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "TNBC microarray data (GSE38959, GSE53752) were retrieved from the Gene Expression Omnibus (GEO) database, and principal component analysis (PCA) was performed to evaluate the reliability of the data."}, {"asset": "source:pmid:40179432", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The intersecting genes underwent Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis to minimize errors and identify TNBC-specific genes."}, {"asset": "source:pmid:40179432", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "There were 10 TNBC-specific genes identified: RRM2, DEPDC1, FIGF, TACC3, E2F1, CDO1, DST, MCM4, CHEK1, and PLSCR4."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GEO microarray data from GSE38959 and GSE53752, LASSO regression analysis identified 10 TNBC-specific genes: RRM2, DEPDC1, FIGF, TACC3, E2F1, CDO1, DST, MCM4, CHEK1, and PLSCR4.", "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:40179432"], "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:40179432", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/18758592241308738", "sha256": "sha256:a08f50447e42ee154f91b16a785076b3e7e4a1dbe25b6664ed5247080bca152f", "bytes": 38132, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/18758592241308738", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12288392", "source": "europe_pmc_fulltext", "coverage": "whole_body", "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": "GSE38959 comprises 30 surgically resected TNBC tissues and 13 normal mammary ductal cells, while GSE53752 consists of 51 TNBC tissues and 25 normal breast tissues.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE38959 comprises 30 surgically resected TNBC tissues and 13 normal mammary ductal cells, while GSE53752 consists of 51 TNBC tissues and 25 normal breast tissues.", "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:GSE53752", "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=GSE53752", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53752", "version": null, "note": "GSE38959 comprises 30 surgically resected TNBC tissues and 13 normal mammary ductal cells, while GSE53752 consists of 51 TNBC tissues and 25 normal breast tissues.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE38959 comprises 30 surgically resected TNBC tissues and 13 normal mammary ductal cells, while GSE53752 consists of 51 TNBC tissues and 25 normal breast tissues.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1299990", "GSM1299991", "GSM1299992", "GSM1299993", "GSM1299994", "GSM1299995", "GSM1299996", "GSM1299997", "GSM1299998", "GSM1299999", "GSM1300000", "GSM1300001", "GSM1300002", "GSM1300003", "GSM1300004", "GSM1300005", "GSM1300006", "GSM1300007", "GSM1300008", "GSM1300009", "GSM1300010", "GSM1300011", "GSM1300012", "GSM1300013", "GSM1300014", "GSM838826", "GSM838827", "GSM838828", "GSM838829", "GSM838830", "GSM838831", "GSM838832", "GSM838833", "GSM838834", "GSM838835", "GSM838836", "GSM838837", "GSM838838", "GSM838839", "GSM838840", "GSM838841", "GSM838842", "GSM838843", "GSM838844", "GSM838845", "GSM838846", "GSM838847", "GSM838848", "GSM838849", "GSM838850", "GSM838851", "GSM838852", "GSM838853", "GSM838854", "GSM838855", "GSM838856", "GSM838857", "GSM838858", "GSM838859", "GSM838860", "GSM838861", "GSM838862", "GSM838863", "GSM838864", "GSM838865", "GSM838866", "GSM838867", "GSM838868", "GSM838869", "GSM838870", "GSM838871", "GSM838872", "GSM838873", "GSM838874", "GSM838875", "GSM838876"], "sample_count": 76, "group_sizes": null, "group_sizes_basis": null, "platform": "7264", "taxon": "Homo sapiens", "title": "Molecular characteristics and metastasis predictor genes of triple-negative breast cancer (II)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE38959 not downloaded", "asset:data:geo:GSE38959 licence not read", "asset:data:geo:GSE53752 not downloaded", "asset:data:geo:GSE53752 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "principal component analysis"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The intersecting genes underwent Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis to minimize errors and identify TNBC-specific genes."}}], "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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", "GSE53752"], "resolved_accessions": ["GSE38959", "GSE53752"], "statements": ["GSE38959 comprises 30 surgically resected TNBC tissues and 13 normal mammary ductal cells, while GSE53752 consists of 51 TNBC tissues and 25 normal breast tissues."], "basis": "The paper names GSE38959, GSE53752 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": ["pca_fit"], "assets": ["source:pmid:40179432", "data:geo:GSE38959"], "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": "2026-11-01T19:49:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 11073, "completion_tokens": 1492, "cached_tokens": 128}}, "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:40179432", "type": "paper", "label": "pmid:40179432"}, {"id": "source:pmid:40179432", "type": "manuscript", "label": "PMID 40179432 full text"}, {"id": "data:geo:GSE38959", "type": "dataset", "label": "GEO GSE38959"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40179432", "type": "paper", "label": "pmid:40179432"}, {"id": "source:pmid:40179432", "type": "manuscript", "label": "PMID 40179432 full text"}, {"id": "data:geo:GSE38959", "type": "dataset", "label": "GEO GSE38959"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40179432", "type": "extraction", "used": ["source:pmid:40179432"], "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:40179432", "parent_hash": "sha256:dd100af0255c400535c4cdee3789f848f33869f845dbfd79a21b505b24142280", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE38959 licence not read", "asset:data:geo:GSE38959 not downloaded", "asset:data:geo:GSE53752 licence not read", "asset:data:geo:GSE53752 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": 0.99, "evidence": ["r triple-negative breast cancer (TNBC). TNBC microarray data (GSE38959, GSE53752) were retrieved fro", "to evaluate the reliability of the data. The microarray datasets were merged, and differentially exp"], "order_basis": "paper_text_order:186", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["3, E2F1, CDO1, DST, MCM4, CHEK1, and PLSCR4. RT-qPCR analysis showed significant upregulation of", "E2F1, CDO1, DST, MCM4, CHEK1, and PLSCR4. RT-qPCR analysis showed significant upregulation of"], "order_basis": "paper_text_order:1168", "id": "assay:2"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["principal component analysis"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}