Identification of Key Genes and Pathways in Triple-Negative Breast Cancer by Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30175120", "kind": "science-record", "revision": 7, "content_hash": "sha256:ba7c5b37d25133ad68a895b668e32521326323a1bae204086140f11701f1f94a", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T22:00:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes and Pathways in Triple-Negative Breast Cancer by Integrated Bioinformatics Analysis.", "doi": "10.1155/2018/2760918", "pmid": "30175120", "authors": ["Pengzhi Dong", "Bing Yu", "Lanlan Pan", "Xiaoxuan Tian", "Fangfang Liu"], "journal": "BioMed research international", "year": 2018, "abstract": "PURPOSE: Triple-negative breast cancer refers to breast cancer that does not express estrogen receptor (ER), progesterone receptor (PR), or human epidermal growth factor receptor 2 (Her2). This study aimed to identify the key pathways and genes and find the potential initiation and progression mechanism of triple-negative breast cancer (TNBC).\nMETHODS: We downloaded the gene expression profiles of GSE76275 from Gene Expression Omnibus (GEO) datasets. This microarray Super-Series sets are composed of gene expression data from 265 samples which included 67 non-TNBC and 198 TNBC. Next, all the differentially expressed genes (DEGs) with p<0.01 and fold change ≥1.5 or ≤-1.5 were identified.\nRESULT: 56 upregulated and 151 downregulated genes were listed and the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis was performed. These significantly changed genes were mainly involved in the biological process termed prostate gland morphogenesis, inner ear morphogenesis, cell maturation, digestive tract morphogenesis, autonomic nervous system development, monovalent inorganic anion homeostasis, neural crest cell development, regulation of dendrite extension and glial cell proliferation, immune system process termed T cell differentiation, regulation of immune response, and macrophage activation. Genes are mainly involved in the KEGG pathway termed Oocyte meiosis. All DEGs underwent survival analysis using datasets from The Cancer Genome Atlas (TCGA) integrated by cBioPortal, of which amplification of SRY-related HMG-box 8 (SOX8), androgen receptor (AR), and Chromosome 9 Open Reading Frame 152 (C9orf152) were significantly negative while Nik Related Kinase (NRK) and RAS oncogene family 30 (RAB30) were positively correlated to the life expectancy (p<0.05).\nCONCLUSIONS: In conclusion, these pathways and genes identified could help understanding the mechanism of development of TNBC. Besides, SOX8, AR, C9orf152, NRK and RAB30, and other key genes and pathways might be promising targets for the TNBC treatment.", "claims": [{"id": "claim-method", "statement": "In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30175120", "locator": "sections[7] \"2.5. Survival Analysis\" paragraph 2", "quote": "In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30175120", "locator": "sections[15] \"Data Availability\" paragraph 2", "quote": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal."}], "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:30175120"], "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:GSE76275"], "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:GSE76275"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30175120", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2018/2760918", "sha256": "sha256:8b81350dccc0bfda8701bc3f76165e42060a4c2b96fafcdd750919225045aa00", "bytes": 35891, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2018/2760918", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6098886", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE76275", "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=GSE76275", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76275", "version": null, "note": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1974566", "GSM1974567", "GSM1974568", "GSM1974569", "GSM1974570", "GSM1974571", "GSM1974572", "GSM1974573", "GSM1974574", "GSM1974575", "GSM1974576", "GSM1974577", "GSM1974578", "GSM1974579", "GSM1974580", "GSM1974581", "GSM1974582", "GSM1974583", "GSM1974584", "GSM1974585", "GSM1974586", "GSM1974587", "GSM1974588", "GSM1974589", "GSM1974590", "GSM1974591", "GSM1974592", "GSM1974593", "GSM1974594", "GSM1974595", "GSM1974596", "GSM1974597", "GSM1974598", "GSM1974599", "GSM1974600", "GSM1974601", "GSM1974602", "GSM1974603", "GSM1974604", "GSM1974605", "GSM1974606", "GSM1974607", "GSM1974608", "GSM1974609", "GSM1974610", "GSM1974611", "GSM1974612", "GSM1974613", "GSM1974614", "GSM1974615", "GSM1974616", "GSM1974617", "GSM1974618", "GSM1974619", "GSM1974620", "GSM1974621", "GSM1974622", "GSM1974623", "GSM1974624", "GSM1974625", "GSM1974626", "GSM1974627", "GSM1974628", "GSM1974629", "GSM1974630", "GSM1974631", "GSM1974632", "GSM1974633", "GSM1974634", "GSM1974635", "GSM1974636", "GSM1974637", "GSM1974638", "GSM1974639", "GSM1974640", "GSM1974641", "GSM1974642", "GSM1974643", "GSM1974644", "GSM1974645", "GSM1974646", "GSM1974647", "GSM1974648", "GSM1974649", "GSM1974650", "GSM1974651", "GSM1974652", "GSM1974653", "GSM1974654", "GSM1974655", "GSM1974656", "GSM1974657", "GSM1974658", "GSM1974659", "GSM1974660", "GSM1974661", "GSM1974662", "GSM1974663", "GSM1974664", "GSM1974665", "GSM1974666", "GSM1974667", "GSM1974668", "GSM1974669", "GSM1974670", "GSM1974671", "GSM1974672", "GSM1974673", "GSM1974674", "GSM1974675", "GSM1974676", "GSM1974677", "GSM1974678", "GSM1974679", "GSM1974680", "GSM1974681", "GSM1974682", "GSM1974683", "GSM1974684", "GSM1974685", "GSM1974686", "GSM1974687", "GSM1974688", "GSM1974689", "GSM1974690", "GSM1974691", "GSM1974692", "GSM1974693", "GSM1974694", "GSM1974695", "GSM1974696", "GSM1974697", "GSM1974698", "GSM1974699", "GSM1974700", "GSM1974701", "GSM1974702", "GSM1974703", "GSM1974704", "GSM1974705", "GSM1974706", "GSM1974707", "GSM1974708", "GSM1974709", "GSM1974710", "GSM1974711", "GSM1974712", "GSM1974713", "GSM1974714", "GSM1974715", "GSM1974716", "GSM1974717", "GSM1974718", "GSM1974719", "GSM1974720", "GSM1974721", "GSM1974722", "GSM1974723", "GSM1974724", "GSM1974725", "GSM1974726", "GSM1974727", "GSM1974728", "GSM1974729", "GSM1974730", "GSM1974731", "GSM1974732", "GSM1974733", "GSM1974734", "GSM1974735", "GSM1974736", "GSM1974737", "GSM1974738", "GSM1974739", "GSM1974740", "GSM1974741", "GSM1974742", "GSM1974743", "GSM1974744", "GSM1974745", "GSM1974746", "GSM1974747", "GSM1974748", "GSM1974749", "GSM1974750", "GSM1974751", "GSM1974752", "GSM1974753", "GSM1974754", "GSM1974755", "GSM1974756", "GSM1974757", "GSM1974758", "GSM1974759", "GSM1974760", "GSM1974761", "GSM1974762", "GSM1974763", "GSM1978883", "GSM1978884", "GSM1978885", "GSM1978886", "GSM1978887", "GSM1978888", "GSM1978889", "GSM1978890", "GSM1978891", "GSM1978892", "GSM1978893", "GSM1978894", "GSM1978895", "GSM1978896", "GSM1978897", "GSM1978898", "GSM1978899", "GSM1978900", "GSM1978901", "GSM1978902", "GSM1978903", "GSM1978904", "GSM1978905", "GSM1978906", "GSM1978907", "GSM1978908", "GSM1978909", "GSM1978910", "GSM1978911", "GSM1978912", "GSM1978913", "GSM1978914", "GSM1978915", "GSM1978916", "GSM1978917", "GSM1978918", "GSM1978919", "GSM1978920", "GSM1978921", "GSM1978922", "GSM1978923", "GSM1978924", "GSM1978925", "GSM1978926", "GSM1978927", "GSM1978928", "GSM1978929", "GSM1978930", "GSM1978931", "GSM1978932", "GSM1978933", "GSM1978934", "GSM1978935", "GSM1978936", "GSM1978937", "GSM1978938", "GSM1978939", "GSM1978940", "GSM1978941", "GSM1978942", "GSM1978943", "GSM1978944", "GSM1978945", "GSM1978946", "GSM1978947", "GSM1978948", "GSM1978949"], "sample_count": 265, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Comprehensive genomic analysis identify novel subtypes and targets of triple-negative breast cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30175120:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:880b98b12d0563f614dc4ad7c96746b284c5b2dcfaf8911ff52d988a97f20b77", "bytes": 590, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#tab1", "version": null, "note": "Cellular component (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 8, "column_count": 4}, "table": {"label": "Table 1", "caption": "Cellular component (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "rows": [["#pathway ID", "pathway description", "observed gene count", "false discovery rate"], ["GO.0005576", "extracellular region", "59", "0.00607"], [""], ["GO.0044421", "extracellular region part", "50", "0.00967"], [""], ["GO.0070062", "extracellular exosome", "41", "0.00967"], [""], ["GO.0031982", "vesicle", "46", "0.0402"]], "row_count": 8, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[10]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:30175120:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:433b0b41ef7fe48f0b6cf91188ac796c537eabf846d4784a21122e3964f293e5", "bytes": 1369, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#tab2", "version": null, "note": "Molecular function (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 18, "column_count": 4}, "table": {"label": "Table 2", "caption": "Molecular function (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "rows": [["#pathway ID", "pathway description", "observed gene count", "false discovery rate"], ["GO.0000977", "RNA polymerase II regulatory region sequence-specific DNA binding", "16", "0.001"], [""], ["GO.0044212", "transcription regulatory region DNA binding", "19", "0.001"], [""], ["GO.0001228", "transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding", "12", "0.00502"], [""], ["GO.0000982", "transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding", "12", "0.00599"], [""], ["GO.0001077", "transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding", "10", "0.00714"], [""], ["GO.0000976", "transcription regulatory region sequence-specific DNA binding", "15", "0.00808"], [""], ["GO.0000981", "RNA polymerase II transcription factor activity, sequence-specific DNA binding", "14", "0.0459"], [""], ["GO.0000987", "core promoter proximal region sequence-specific DNA binding", "10", "0.0459"], [""], ["GO.0001158", "enhancer sequence-specific DNA binding", "5", "0.0459"]], "row_count": 18, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[10]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:30175120:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0278b31afd7fc370d78c1fe600de800b6184f75bac2f839ef49e1fcaf04af7c5", "bytes": 941, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[3]#tab3", "version": null, "note": "Biological process (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 18, "column_count": 4}, "table": {"label": "Table 3", "caption": "Biological process (GO) enrichment analysis result of differentially expressed genes (DEGs) with fold change ≥1.5 or ≤-1.5 and p<0.01.", "rows": [["#pathway ID", "pathway description", "observed gene count", "false discovery rate"], ["GO.0014032", "neural crest cell development", "6", "0.0203"], [""], ["GO.0014033", "neural crest cell differentiation", "6", "0.0203"], [""], ["GO.0030855", "epithelial cell differentiation", "15", "0.0203"], [""], ["GO.0040007", "growth", "14", "0.0203"], [""], ["GO.0048589", "developmental growth", "12", "0.0203"], [""], ["GO.0051094", "positive regulation of developmental process", "23", "0.0203"], [""], ["GO.0060429", "epithelium development", "22", "0.0203"], [""], ["GO.0042127", "regulation of cell proliferation", "27", "0.0239"], [""], ["GO.0002064", "epithelial cell development", "9", "0.0382"]], "row_count": 18, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[10]/table-wrap[3]#tab3"}}, {"id": "asset:table:pmid:30175120:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dadf33dfe2e215a64cbd1a13d3d53c48aae2001429aaf758b8c017d9fd460a19", "bytes": 495, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[4]#tab4", "version": null, "note": "KEGG pathway analysis", "structure": {"pmcid": "PMC6098886", "section_index": 10, "section_title": "3.2. Gene Ontology (GO) Term Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of DEGs", "row_count": 20, "column_count": 2}, "table": {"label": "Table 4", "caption": "KEGG pathway analysis", "rows": [["Category", "KEGG_PATHWAY"], ["Term", "hsa04114: Oocyte meiosis"], [""], ["Count", "4"], [""], ["%", "0.016343875"], [""], ["P Value", "0.0711977"], [""], ["Genes", "PGR, AR, BUB1, CDC20"], [""], ["List Total", "62"], [""], ["Pop Hits", "109"], [""], ["Pop Total", "6910"], [""], ["Fold Enrichment", "4.089967446"], [""], ["Bonferroni", "0.999835961"]], "row_count": 20, "column_count": 2, "numeric_cells": 10, "header_rows": 1, "locator": "section[10]/table-wrap[4]#tab4"}}], "gaps": ["asset:data:geo:GSE76275 not downloaded", "asset:data:geo:GSE76275 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database."}}, {"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": 0.8, "band": "high", "quote": "Protein-Protein Interaction"}}, {"id": "method-3", "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": "Pathway Enrichment"}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE76275"], "resolved_accessions": ["GSE76275"], "statements": ["Data Availability For GEO data downloading, readers can visit the website https://www.ncbi.nlm.nih.gov/ and choose “GEO datasets” in the drop-down list.For gene enrichment analysis, a web based tool DAVID (https://david.ncifcrf.gov/) was used.For inferring the protein-protein interaction, we use web based tool named STRING (https://string-db.org/) according to the instruction. For drawing the network, Cytoscape 3.5 was used. For life span expectation analysis, we visit cBioportal."], "basis": "The paper names GSE76275 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": ["survival_km"], "assets": ["source:pmid:30175120", "data:geo:GSE76275", "asset:table:pmid:30175120:1", "asset:table:pmid:30175120:2", "asset:table:pmid:30175120:3", "asset:table:pmid:30175120:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE76275"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29916, "completion_tokens": 1613, "cached_tokens": 10248}}, "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:30175120", "type": "paper", "label": "pmid:30175120"}, {"id": "source:pmid:30175120", "type": "manuscript", "label": "PMID 30175120 full text"}, {"id": "data:geo:GSE76275", "type": "dataset", "label": "GEO GSE76275"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30175120", "type": "paper", "label": "pmid:30175120"}, {"id": "source:pmid:30175120", "type": "manuscript", "label": "PMID 30175120 full text"}, {"id": "data:geo:GSE76275", "type": "dataset", "label": "GEO GSE76275"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30175120", "type": "extraction", "used": ["source:pmid:30175120"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE76275", "type": "accession_resolution", "used": ["data:geo:GSE76275"], "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:30175120", "parent_hash": "sha256:c1dc34efb8b2fe2f23e089013d90dc14b5dc3474cbb0b887fa3cecae54ef1b84", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE76275 licence not read", "asset:data:geo:GSE76275 not downloaded", "execution.not_run", "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": ["Gene Expression Omnibus (GEO) datasets. This microarray Super-Series sets are composed of gene expre"], "order_basis": "paper_text_order:528", "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": 1.0, "evidence": ["In this study, survival analysis refers to the Overall Survival Kaplan-Meier Estimate. Survival analysis was performed using datasets termed Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) from cBioPortal database."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}