Identification of Hub Genes and Pathways of Triple Negative Breast Cancer by Expression Profiles Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33688252", "kind": "science-record", "revision": 8, "content_hash": "sha256:8193384a190d5491c4d006811fff09eae3a65c1a6d90310269f5cc63ee163ffb", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T22:03:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes and Pathways of Triple Negative Breast Cancer by Expression Profiles Analysis.", "doi": "10.2147/CMAR.S295951", "pmid": "33688252", "authors": ["Liqi Li", "Hu Huang", "Mingjie Zhu", "Junqiang Wu"], "journal": "Cancer management and research", "year": 2021, "abstract": "PURPOSE: Triple negative breast cancer (TNBC) is an intrinsic subtype of breast cancer with a poor prognosis, characterized by a lack of ER and PR expression and the absence of HER2 amplification. The aim of this study is to characterize hub genes (key genes in the molecular interaction network) expression in TNBC, which may serve as prognostic predictors for TNBC treatment.\nMETHODS: Four transcriptome microarray datasets GSE27447, GSE39004, GSE43358 and GSE45827 were obtained from the Gene Expression Omnibus (GEO) database, and R package limma and RobustRankAggreg were employed to identify common differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted by DAVID and KOBAS database. Thereafter, protein-protein interaction (PPI) network was constructed according to STRING online database. Functional modules and hub genes were screened by MCODE and cytohubba plug-ins, and the Cancer Genome Atlas (TCGA) survival analysis and qRT-PCR were utilized to validate the expression of these hub genes on TNBC.\nRESULTS: A total of 134 DEGs were identified by differential expression analysis, consisting of 88 up- and 46 down-regulated genes. GO and KEGG analyses showed that the terms and pathways enriched were mainly associated with cell adhesion, tumorigenesis and cellular immunity. From the PPI network, we identified six hub genes, including CD3D, CD3E, CD3G, FYN, GRAP2 and ITK. Survival analysis and the qRT-PCR results confirmed the robustness of the identified hub genes.\nCONCLUSION: This study provides a new insight into the understanding of the molecular mechanisms associated with TNBC and suggested that the hub genes may serve as prognostic predictors.", "claims": [{"id": "claim-data-access", "statement": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33688252", "locator": "sections[3] \"Downloading and Processing of Microarray Datasets\" paragraph 2", "quote": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis."}], "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:33688252"], "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:GSE27447"], "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:GSE27447"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33688252", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S295951", "sha256": "sha256:3c531c7fc149fa9803bab7d936902393365bab03203a9d9b71f83daaee9c06f2", "bytes": 22121, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S295951", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7935333", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE27447", "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=GSE27447", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27447", "version": null, "note": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM678364", "GSM678365", "GSM678366", "GSM678367", "GSM678368", "GSM678369", "GSM678370", "GSM678371", "GSM678372", "GSM678373", "GSM678374", "GSM678375", "GSM678376", "GSM678377", "GSM678378", "GSM678379", "GSM678380", "GSM678381", "GSM678382"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "FZD7 Plays a Critical Role in Triple Negative Breast Cancer Proliferation", "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:GSE39004", "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=GSE39004", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39004", "version": null, "note": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM926963", "GSM926964", "GSM926965", "GSM926966", "GSM926967", "GSM926968", "GSM926969", "GSM926970", "GSM926971", "GSM926972", "GSM926973", "GSM926974", "GSM926975", "GSM926976", "GSM926977", "GSM926978", "GSM926979", "GSM926980", "GSM926981", "GSM926982", "GSM926983", "GSM926984", "GSM926985", "GSM926986", "GSM926987", "GSM926988", "GSM926989", "GSM926990", "GSM926991", "GSM926992", "GSM926993", "GSM926994", "GSM926995", "GSM926996", "GSM926997", "GSM926998", "GSM926999", "GSM927000", "GSM927001", "GSM927002", "GSM927003", "GSM927004", "GSM927005", "GSM927006", "GSM927007", "GSM927008", "GSM927009", "GSM927010", "GSM927011", "GSM927012", "GSM927013", "GSM927014", "GSM927015", "GSM927016", "GSM927017", "GSM927018", "GSM927019", "GSM927020", "GSM927021", "GSM927022", "GSM927023", "GSM927024", "GSM927025", "GSM927026", "GSM927027", "GSM927028", "GSM927029", "GSM927030", "GSM927031", "GSM927032", "GSM927033", "GSM927034", "GSM927035", "GSM927036", "GSM927037", "GSM927038", "GSM927039", "GSM927040", "GSM927041", "GSM927042", "GSM927043", "GSM927044", "GSM927045", "GSM927046", "GSM927047", "GSM927048", "GSM927049", "GSM927050", "GSM927051", "GSM927052", "GSM927053", "GSM927054", "GSM927055", "GSM927056", "GSM927057", "GSM927058", "GSM927059", "GSM927060", "GSM927061", "GSM927062", "GSM927063", "GSM927064", "GSM927065", "GSM927066", "GSM927067", "GSM927068", "GSM927069", "GSM927070", "GSM927093", "GSM927094", "GSM927095", "GSM927096", "GSM927097", "GSM927098", "GSM927099", "GSM927100", "GSM927101", "GSM927102", "GSM927103", "GSM927104", "GSM927105", "GSM927106", "GSM927107", "GSM927108", "GSM927109", "GSM927110", "GSM927111", "GSM927112", "GSM927113", "GSM927114", "GSM927115", "GSM927116", "GSM927117", "GSM927118", "GSM927119", "GSM927120", "GSM927121", "GSM927122", "GSM927123", "GSM927124", "GSM927125", "GSM927126", "GSM927127", "GSM927128", "GSM927129", "GSM927130", "GSM927131", "GSM927132", "GSM927133", "GSM927134", "GSM927135", "GSM927136", "GSM927137", "GSM927138", "GSM927139", "GSM927140", "GSM927141", "GSM927142", "GSM927143", "GSM927144", "GSM927145", "GSM927146", "GSM927147", "GSM927148", "GSM927149", "GSM927150", "GSM927151", "GSM927152", "GSM927153", "GSM927154", "GSM927155", "GSM927156", "GSM927157", "GSM927158", "GSM927159", "GSM927160", "GSM927161", "GSM927162", "GSM927163", "GSM927164"], "sample_count": 180, "group_sizes": null, "group_sizes_basis": null, "platform": "13534;6244", "taxon": "Homo sapiens", "title": "Molecular Profiles of Human Breast Cancer and Their Association with Tumor Subtypes and Disease Prognosis", "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:GSE43358", "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=GSE43358", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43358", "version": null, "note": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1060909", "GSM1060910", "GSM1060911", "GSM1060912", "GSM1060913", "GSM1060914", "GSM1060915", "GSM1060916", "GSM1060917", "GSM1060918", "GSM1060919", "GSM1060920", "GSM1060921", "GSM1060922", "GSM1060923", "GSM1060924", "GSM1060925", "GSM1060926", "GSM1060927", "GSM1060928", "GSM1060929", "GSM1060930", "GSM1060931", "GSM1060932", "GSM1060933", "GSM1060934", "GSM1060936", "GSM1060937", "GSM1060938", "GSM1060939", "GSM1060940", "GSM1060941", "GSM1060942", "GSM1060943", "GSM1060944", "GSM1060945", "GSM1060946", "GSM1060947", "GSM1060948", "GSM1060949", "GSM1060950", "GSM1060951", "GSM1060952", "GSM1060953", "GSM1060954", "GSM1060955", "GSM1060956", "GSM1060957", "GSM1060958", "GSM1060959", "GSM1060960", "GSM1060961", "GSM1060962", "GSM1060963", "GSM1060964", "GSM1060965", "GSM1060966"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology", "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": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1116084", "GSM1116085", "GSM1116086", "GSM1116087", "GSM1116088", "GSM1116089", "GSM1116090", "GSM1116091", "GSM1116092", "GSM1116093", "GSM1116094", "GSM1116095", "GSM1116096", "GSM1116097", "GSM1116098", "GSM1116099", "GSM1116100", "GSM1116101", "GSM1116102", "GSM1116103", "GSM1116104", "GSM1116105", "GSM1116106", "GSM1116107", "GSM1116108", "GSM1116109", "GSM1116110", "GSM1116111", "GSM1116112", "GSM1116113", "GSM1116114", "GSM1116115", "GSM1116116", "GSM1116117", "GSM1116118", "GSM1116119", "GSM1116120", "GSM1116121", "GSM1116122", "GSM1116123", "GSM1116124", "GSM1116125", "GSM1116126", "GSM1116127", "GSM1116128", "GSM1116129", "GSM1116130", "GSM1116131", "GSM1116132", "GSM1116133", "GSM1116134", "GSM1116135", "GSM1116136", "GSM1116137", "GSM1116138", "GSM1116139", "GSM1116140", "GSM1116141", "GSM1116142", "GSM1116143", "GSM1116144", "GSM1116145", "GSM1116146", "GSM1116147", "GSM1116148", "GSM1116149", "GSM1116150", "GSM1116151", "GSM1116152", "GSM1116153", "GSM1116154", "GSM1116155", "GSM1116156", "GSM1116157", "GSM1116158", "GSM1116159", "GSM1116160", "GSM1116161", "GSM1116162", "GSM1116163", "GSM1116164", "GSM1116165", "GSM1116166", "GSM1116167", "GSM1116168", "GSM1116169", "GSM1116170", "GSM1116171", "GSM1116172", "GSM1116173", "GSM1116174", "GSM1116175", "GSM1116176", "GSM1116177", "GSM1116178", "GSM1116179", "GSM1116180", "GSM1116181", "GSM1116182", "GSM1116183", "GSM1116184", "GSM1116185", "GSM1116186", "GSM1116187", "GSM1116188", "GSM1116189", "GSM1116190", "GSM1116191", "GSM1116192", "GSM1116193", "GSM1116194", "GSM1116195", "GSM1116196", "GSM1116197", "GSM1116198", "GSM1116199", "GSM1116200", "GSM1116201", "GSM1116202", "GSM1116203", "GSM1116204", "GSM1116205", "GSM1116206", "GSM1116207", "GSM1116208", "GSM1116209", "GSM1116210", "GSM1116211", "GSM1116212", "GSM1116213", "GSM1116214", "GSM1116215", "GSM1116216", "GSM1116217", "GSM1116218", "GSM1116219", "GSM1116220", "GSM1116221", "GSM1116222", "GSM1116223", "GSM1116224", "GSM1116225", "GSM1116226", "GSM1116227", "GSM1116228", "GSM1116229", "GSM1116230", "GSM1116231", "GSM1116232", "GSM1116233", "GSM1116234", "GSM1116235", "GSM1116236", "GSM1116237", "GSM1116238"], "sample_count": 155, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from Breast cancer subtypes", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33688252:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:838603d983e81e6a3b41ca718d505e364b8fece52d9cf48dc77a6dddce33ea03", "bytes": 890, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0001", "version": null, "note": "KEGG Enrichment Analysis of Top four Modules Identified from PPI Network", "structure": {"pmcid": "PMC7935333", "section_index": 13, "section_title": "PPI Network Construction and Hub Gene Identification", "row_count": 11, "column_count": 5}, "table": {"label": "Table 1", "caption": "KEGG Enrichment Analysis of Top four Modules Identified from PPI Network", "rows": [["Module", "KEGG Entry", "Description", "Count", "FDR"], ["Module 1", "hsa04660", "T cell receptor signaling pathway", "8", "2.06E-13"], ["", "hsa04664", "Fc epsilon RI signaling pathway", "2", "0.001979"], ["Module 2", "hsa04974", "Protein digestion and absorption", "6", "1.51E-11"], ["", "hsa04512", "ECM-receptor interaction", "6", "1.51E-11"], ["", "hsa04510", "Focal adhesion", "6", "1.89E-09"], ["Module 3", "hsa04512", "ECM-receptor interaction", "4", "2.03E-07"], ["", "hsa04510", "Focal adhesion", "4", "4.12E-06"], ["", "hsa04514", "Cell adhesion molecules (CAMs)", "3", "0.000126"], ["Module 4", "hsa05200", "Pathways in cancer", "3", "0.006485"], ["", "hsa04012", "ErbB signaling pathway", "2", "0.007474"]], "row_count": 11, "column_count": 5, "numeric_cells": 34, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t0001"}}], "gaps": ["asset:data:geo:GSE27447 not downloaded", "asset:data:geo:GSE27447 licence not read", "asset:data:geo:GSE39004 not downloaded", "asset:data:geo:GSE39004 licence not read", "asset:data:geo:GSE43358 not downloaded", "asset:data:geo:GSE43358 licence not read", "asset:data:geo:GSE45827 not downloaded", "asset:data:geo:GSE45827 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-3", "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"}}, {"id": "method-4", "family": null, "specific": null, "label": "Robust rank aggregation (RRA) applied to four microarray datasets downloaded from the Gene Expression Omnibus (GEO) database", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“Furthermore, to screen out the common DEGs from all these datasets, we employed the robust rank aggregation (RRA) analysis by applying R package RobustRankAggreg (https://cran.r-project.org/web/packages/RobustRankAggreg/index.html).” “Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis.”"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE27447", "GSE39004", "GSE43358", "GSE45827"], "resolved_accessions": ["GSE27447", "GSE39004", "GSE43358", "GSE45827"], "statements": ["Microarray datasets (GSE27447,13 GSE39004,14 GSE4335815 and GSE4582716) were downloaded from GEO (URL: http://www.ncbi.nlm.nih.gov/geo) database for differential expression analysis."], "basis": "The paper names GSE27447, GSE39004, GSE43358, GSE45827 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": ["cox_ph"], "assets": ["source:pmid:33688252", "data:geo:GSE27447", "asset:table:pmid:33688252:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE27447"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:44Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 16785, "completion_tokens": 2099, "cached_tokens": 520}}, "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:33688252", "type": "paper", "label": "pmid:33688252"}, {"id": "source:pmid:33688252", "type": "manuscript", "label": "PMID 33688252 full text"}, {"id": "data:geo:GSE27447", "type": "dataset", "label": "GEO GSE27447"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33688252", "type": "paper", "label": "pmid:33688252"}, {"id": "source:pmid:33688252", "type": "manuscript", "label": "PMID 33688252 full text"}, {"id": "data:geo:GSE27447", "type": "dataset", "label": "GEO GSE27447"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33688252", "type": "extraction", "used": ["source:pmid:33688252"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE27447", "type": "accession_resolution", "used": ["data:geo:GSE27447"], "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:33688252", "parent_hash": "sha256:eb3069a9eacba4111f88f50e82d3a607f4dc9fdb528acd926038df3e1dee2607", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE27447 licence not read", "asset:data:geo:GSE27447 not downloaded", "asset:data:geo:GSE39004 licence not read", "asset:data:geo:GSE39004 not downloaded", "asset:data:geo:GSE43358 licence not read", "asset:data:geo:GSE43358 not downloaded", "asset:data:geo:GSE45827 licence not read", "asset:data:geo:GSE45827 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": ["TNBC treatment. METHODS: Four transcriptome microarray datasets GSE27447, GSE39004, GSE43358 and GS"], "order_basis": "paper_text_order:469", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Cox regression"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}