Identification of Biomarkers in Breast Cancer by Gene Expression Profiling Using Human Tissues.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25396118", "kind": "science-record", "revision": 3, "content_hash": "sha256:35767fdb3a5633cc0a700b12cdcfa65e60e32fc5cd22133018f423f222323f7d", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:19:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Biomarkers in Breast Cancer by Gene Expression Profiling Using Human Tissues.", "doi": "10.1016/j.gdata.2014.09.004", "pmid": "25396118", "authors": ["Junjie Fu", "William Allen", "Amy Xia", "Zhuofan Ma", "Xin Qi"], "journal": "Genomics data", "year": 2014, "abstract": "Breast cancer is the second leading cause of death by cancer in women. To identify biomarkers with potential diagnostic and therapeutic utilities in breast cancer, gene expression profiling from real patient tissues were used to discover significantly deregulated genes out of 50,739 genes of human transcriptome. Total RNAs were extracted, and the gene expression profiles of 32 cancerous and normal tissues were established using Agilent gene expression microarray technology. The results were analyzed with Agilent GeneSpring 12.6 software. Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297.", "claims": [{"id": "claim-method", "statement": "Plots are generated using GeneSpring 12.6 with moderated t-test and Benjamini –Hochberg testing correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25396118", "locator": "sections[10] \"Differential expression\" paragraph 3", "quote": "Plots are generated using GeneSpring 12.6 with moderated t-test and Benjamini –Hochberg testing correction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25396118", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper identified 779 genes with corrected p-value ≤ 0.05 and at least twofold change in all three breast cancer subtypes using one-way ANOVA with Benjamini–Hochberg correction, while subgroup volcano plots used a moderated t-test; the underlying microarray data were deposited in GEO under accession GSE57297 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57297.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25396118", "locator": "sections[10] \"Differential expression\" paragraph 4", "quote": "Furthermore, 779 genes were identified with p-value ≤ 0.05 (One-Way ANOVA with asymptotic computation and Benjamin–Hochberg multiple testing corrections) and fold change ≥ 2 [8], [9] in all three breast cancer subtypes."}, {"asset": "source:pmid:25396118", "locator": "sections[10] \"Differential expression\" paragraph 2", "quote": "The moderated t-test is one of the statistical tests provided by the GeneSpring 12.6 software as a modification of the unpaired t-test (Agilent GeneSpring 12.6 manual, 22.3.7, P589)."}, {"asset": "source:pmid:25396118", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297."}, {"asset": "source:pmid:25396118", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57297"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper identified 779 genes with corrected p-value ≤ 0.05 and at least twofold change in all three breast cancer subtypes using one-way ANOVA with Benjamini–Hochberg correction, while subgroup volcano plots used a moderated t-test; the underlying microarray data were deposited in GEO under accession GSE57297 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57297.", "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:25396118"], "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:GSE57297"], "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:GSE57297"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25396118", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2014.09.004", "sha256": "sha256:9ffd31464bcc4aedf2cb553161fcaa539326ef73cf024c5e47310148ae8bcdcf", "bytes": 9790, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2014.09.004", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4226530", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57297", "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=GSE57297", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57297", "version": null, "note": "Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1378979", "GSM1378980", "GSM1378981", "GSM1378982", "GSM1378983", "GSM1378984", "GSM1378985", "GSM1378986", "GSM1378987", "GSM1378988", "GSM1378989", "GSM1378990", "GSM1378991", "GSM1378992", "GSM1378993", "GSM1378994", "GSM1378995", "GSM1378996", "GSM1378997", "GSM1378998", "GSM1378999", "GSM1379000", "GSM1379001", "GSM1379002", "GSM1379003", "GSM1379004", "GSM1379005", "GSM1379006", "GSM1379007", "GSM1379008", "GSM1379009", "GSM1379010"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Identification of significant gene regulations for breast cancer from human tissues", "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:GSE57297 not downloaded", "asset:data:geo:GSE57297 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Moderated t-test with Benjamini–Hochberg testing correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Plots are generated using GeneSpring 12.6 with moderated t-test and Benjamini –Hochberg testing correction."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Moderated t-test with Benjamini–Hochberg testing correction), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE57297"], "resolved_accessions": ["GSE57297"], "statements": ["Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297."], "basis": "The paper names GSE57297 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": [], "assets": ["source:pmid:25396118", "data:geo:GSE57297"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE57297"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:23:03Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 24804, "completion_tokens": 3005, "cached_tokens": 1824}}, "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:25396118", "type": "paper", "label": "pmid:25396118"}, {"id": "source:pmid:25396118", "type": "manuscript", "label": "PMID 25396118 full text"}, {"id": "data:geo:GSE57297", "type": "dataset", "label": "GEO GSE57297"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25396118", "type": "paper", "label": "pmid:25396118"}, {"id": "source:pmid:25396118", "type": "manuscript", "label": "PMID 25396118 full text"}, {"id": "data:geo:GSE57297", "type": "dataset", "label": "GEO GSE57297"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25396118", "type": "extraction", "used": ["source:pmid:25396118"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE57297", "type": "accession_resolution", "used": ["data:geo:GSE57297"], "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:25396118", "parent_hash": "sha256:278fd668829bc0fb114030cc470c36880014800b88120909395206c51b99eacd", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE57297 licence not read", "asset:data:geo:GSE57297 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": ["re established using Agilent gene expression microarray technology. The results were analyzed with A", "ed experimental methods and analysis for the microarray data, which have been deposited into Gene Ex"], "order_basis": "paper_text_order:507", "id": "assay:1"}]}