{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34900411", "kind": "science-record", "revision": 5, "content_hash": "sha256:531975206484ec4169fe857c5600fc5570ec89439ab47674b47ad92214ccc535", "created_at": "2026-11-01T17:36:37Z", "updated_at": "2026-11-01T22:48:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer.", "doi": "10.7717/peerj.12383", "pmid": "34900411", "authors": ["Peng Su", "Ziqi Peng", "Boyang Xu", "Bowen Yang", "Feng Jin"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Recently, researchers have classified highly heterogeneous triple negative breast cancer (TNBC) into different subtypes from different perspectives and investigated the characteristics of different subtypes to pursue individualized treatment. With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration.\nMETHOD: The fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs.\nRESULTS: Five hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes and N staging as prognostic factors. The results of ROC and decision curve analyses showed that this model had high prediction accuracy and patients could benefit therefrom. Finally, GDSC database analysis proved that patients in Cluster A were more sensitive to Vinorelbine. Separate analysis of the sensitivity of patients in Cluster A to Gemcitabine and Vinorelbine showed that the patients in Cluster A exhibited higher sensitivity to Vinorelbine. We hypothesized that these five genes were related to gemcitabine resistance and they could serve as biomarkers for clinical drug decision-making after anthracene resistance and taxane resistance in patients with advanced TNBC.\nCONCLUSION: This study found five hub prognostic genes associated with macrophages, and a prognostic model was established to predict the survival of TNBC patients. Finally, these five genes were related to gemcitabine resistance in TNBC patients.", "claims": [{"id": "claim-method", "statement": "Time-dependent ROC curves were used to study the predictive power of the prognostic model", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34900411", "locator": "sections[19] \"Construction and test of prognosis model based on hub genes\" paragraph 2", "quote": "Time-dependent ROC curves were used to study the predictive power of the prognostic model"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34900411", "locator": "sections[34] \"Data Availability Statement\" paragraphs 1-5", "quote": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Time-dependent ROC curves were used to study the predictive power of the prognostic model, and the AUC values at one year, three years, five years, seven years, and ten years were 0.77, 0.58, 0.71, 0.75, and 0.96 (Fig. 7B).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34900411", "locator": "sections[19] \"Construction and test of prognosis model based on hub genes\" paragraph 2", "quote": "Time-dependent ROC curves were used to study the predictive power of the prognostic model, and the AUC values at one year, three years, five years, seven years, and ten years were 0.77, 0.58, 0.71, 0.75, and 0.96 (Fig. 7B)."}, {"asset": "source:pmid:34900411", "locator": "sections[19] \"Construction and test of prognosis model based on hub genes\" paragraph 2", "quote": "The prediction results of the model proposed in this study closely matched the real value without statistically significant differences, showing that this prognostic model had high prediction accuracy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Time-dependent ROC curves were used to study the predictive power of the prognostic model, and the AUC values at one year, three years, five years, seven years, and ten years were 0.77, 0.58, 0.71, 0.75, and 0.96 (Fig. 7B).", "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:34900411"], "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:GSE103091"], "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:GSE103091"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34900411", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.12383", "sha256": "sha256:c8f2225ed4e196477f769f145ac639632451d0355337ecc30dad1ba4b7a7ba8c", "bytes": 62692, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.12383", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8621725", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE103091", "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=GSE103091", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE103091", "version": null, "note": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1419942", "GSM1419943", "GSM1419944", "GSM1419945", "GSM1419946", "GSM1419947", "GSM1419948", "GSM1419949", "GSM1419950", "GSM1419951", "GSM1419952", "GSM1419953", "GSM1419954", "GSM1419955", "GSM1419956", "GSM1419957", "GSM1419958", "GSM1419968", "GSM1419969", "GSM1419970", "GSM1419971", "GSM1419972", "GSM1419973", "GSM1419974", "GSM1419975", "GSM1419976", "GSM1419977", "GSM1419978", "GSM1419979", "GSM1419980", "GSM1419981", "GSM1419982", "GSM1419983", "GSM1419984", "GSM1419985", "GSM1419986", "GSM1419987", "GSM1419988", "GSM1419989", "GSM1419990", "GSM1419991", "GSM1419992", "GSM1419993", "GSM1419994", "GSM1419995", "GSM1419996", "GSM1419997", "GSM1419998", "GSM1419999", "GSM1420000", "GSM1420001", "GSM1420002", "GSM1420003", "GSM1420004", "GSM1420005", "GSM1420006", "GSM1420007", "GSM1420008", "GSM1420009", "GSM1420010", "GSM1420011", "GSM1420012", "GSM1420013", "GSM1420014", "GSM1420015", "GSM1420016", "GSM1420017", "GSM1420018", "GSM1420019", "GSM1420020", "GSM1420021", "GSM1420022", "GSM1420023", "GSM1420024", "GSM1420025", "GSM1420026", "GSM1420027", "GSM1420028", "GSM1420029", "GSM1420030", "GSM1420031", "GSM1420032", "GSM1420033", "GSM1420034", "GSM1420035", "GSM1420036", "GSM1420037", "GSM1420038", "GSM1420039", "GSM1420040", "GSM1420041", "GSM1420042", "GSM1420043", "GSM1420044", "GSM1420045", "GSM1420046", "GSM1420047", "GSM1420048", "GSM1420049", "GSM1420050", "GSM1420051", "GSM1420052", "GSM1420053", "GSM1420054", "GSM1420055", "GSM1420056", "GSM1420057", "GSM2202783", "GSM2202784", "GSM2202785", "GSM2202786", "GSM2202787", "GSM2202788", "GSM2202789", "GSM2202790", "GSM2202791", "GSM2202792", "GSM2202793", "GSM2202794", "GSM2202795", "GSM2202796", "GSM2202797", "GSM2202798", "GSM2202799", "GSM2202800", "GSM2202801", "GSM2202802", "GSM2202803", "GSM2202804", "GSM2202805", "GSM2202806", "GSM2202807", "GSM2202808", "GSM2202809", "GSM2202810", "GSM2202811", "GSM2202812", "GSM2202813", "GSM2202814", "GSM2202815", "GSM2202816", "GSM2202817", "GSM2202818", "GSM2202819", "GSM2202820", "GSM2202821", "GSM2202822", "GSM2202823", "GSM2202824", "GSM2202825", "GSM2202826", "GSM2202827", "GSM2202828", "GSM2202829", "GSM2202830", "GSM2202831", "GSM2202832", "GSM2202833", "GSM2202834", "GSM2202835", "GSM2202836", "GSM2202837", "GSM2202838", "GSM2202839", "GSM2202840", "GSM2202841", "GSM2202842", "GSM2202843", "GSM2202844", "GSM2202845", "GSM2202846", "GSM2202847", "GSM2202848", "GSM2202849", "GSM2202850", "GSM2202851", "GSM2202852", "GSM2202853", "GSM2202854", "GSM2202855", "GSM2202856", "GSM2202857", "GSM2202858", "GSM2202859", "GSM2202860", "GSM2202861", "GSM2202862", "GSM2202863", "GSM2202864", "GSM2202865", "GSM2202866", "GSM2202867", "GSM2202868", "GSM2202869", "GSM2202870", "GSM2202871", "GSM2202872", "GSM2202873", "GSM2202874", "GSM2202875", "GSM2202876", "GSM2202877", "GSM2202878", "GSM2202879", "GSM2202880", "GSM2202881", "GSM2202882", "GSM2202883", "GSM2202884", "GSM2202885", "GSM2202886", "GSM2202887", "GSM2202888", "GSM2202889", "GSM2202890", "GSM2202891", "GSM2202892", "GSM2202893", "GSM2202894", "GSM2202895", "GSM2202896", "GSM2202897", "GSM2202898", "GSM2202899", "GSM2202900", "GSM2202901", "GSM2202902", "GSM2202903", "GSM2202904", "GSM2202905", "GSM2202906", "GSM2202907", "GSM2202908", "GSM2202909", "GSM2202910", "GSM2202911", "GSM2202912", "GSM2202913"], "sample_count": 238, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene-expression molecular subtyping of triple-negative breast cancer tumors", "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:GSE118389", "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=GSE118389", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE118389", "version": null, "note": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3326172", "GSM3326173", "GSM3326174", "GSM3326175", "GSM3326176", "GSM3326177", "GSM3326178", "GSM3326179", "GSM3326180", "GSM3326181", "GSM3326182", "GSM3326183", "GSM3326184", "GSM3326185", "GSM3326186", "GSM3326187", "GSM3326188", "GSM3326189", "GSM3326190", "GSM3326191", "GSM3326192", "GSM3326193", "GSM3326194", "GSM3326195", "GSM3326196", "GSM3326197", "GSM3326198", "GSM3326199", "GSM3326200", "GSM3326201", "GSM3326202", "GSM3326203", "GSM3326204", "GSM3326205", "GSM3326206", "GSM3326207", "GSM3326208", "GSM3326209", "GSM3326210", "GSM3326211", "GSM3326212", "GSM3326213", "GSM3326214", "GSM3326215", "GSM3326216", "GSM3326217", "GSM3326218", "GSM3326219", "GSM3326220", "GSM3326221", "GSM3326222", "GSM3326223", "GSM3326224", "GSM3326225", "GSM3326226", "GSM3326227", "GSM3326228", "GSM3326229", "GSM3326230", "GSM3326231", "GSM3326232", "GSM3326233", "GSM3326234", "GSM3326235", "GSM3326236", "GSM3326237", "GSM3326238", "GSM3326239", "GSM3326240", "GSM3326241", "GSM3326242", "GSM3326243", "GSM3326244", "GSM3326245", "GSM3326246", "GSM3326247", "GSM3326248", "GSM3326249", "GSM3326250", "GSM3326251", "GSM3326252", "GSM3326253", "GSM3326254", "GSM3326255", "GSM3326256", "GSM3326257", "GSM3326258", "GSM3326259", "GSM3326260", "GSM3326261", "GSM3326262", "GSM3326263", "GSM3326264", "GSM3326265", "GSM3326266", "GSM3326267", "GSM3326268", "GSM3326269", "GSM3326270", "GSM3326271", "GSM3326272", "GSM3326273", "GSM3326274", "GSM3326275", "GSM3326276", "GSM3326277", "GSM3326278", "GSM3326279", "GSM3326280", "GSM3326281", "GSM3326282", "GSM3326283", "GSM3326284", "GSM3326285", "GSM3326286", "GSM3326287", "GSM3326288", "GSM3326289", "GSM3326290", "GSM3326291", "GSM3326292", "GSM3326293", "GSM3326294", "GSM3326295", "GSM3326296", "GSM3326297", "GSM3326298", "GSM3326299", "GSM3326300", "GSM3326301", "GSM3326302", "GSM3326303", "GSM3326304", "GSM3326305", "GSM3326306", "GSM3326307", "GSM3326308", "GSM3326309", "GSM3326310", "GSM3326311", "GSM3326312", "GSM3326313", "GSM3326314", "GSM3326315", "GSM3326316", "GSM3326317", "GSM3326318", "GSM3326319", "GSM3326320", "GSM3326321", "GSM3326322", "GSM3326323", "GSM3326324", "GSM3326325", "GSM3326326", "GSM3326327", "GSM3326328", "GSM3326329", "GSM3326330", "GSM3326331", "GSM3326332", "GSM3326333", "GSM3326334", "GSM3326335", "GSM3326336", "GSM3326337", "GSM3326338", "GSM3326339", "GSM3326340", "GSM3326341", "GSM3326342", "GSM3326343", "GSM3326344", "GSM3326345", "GSM3326346", "GSM3326347", "GSM3326348", "GSM3326349", "GSM3326350", "GSM3326351", "GSM3326352", "GSM3326353", "GSM3326354", "GSM3326355", "GSM3326356", "GSM3326357", "GSM3326358", "GSM3326359", "GSM3326360", "GSM3326361", "GSM3326362", "GSM3326363", "GSM3326364", "GSM3326365", "GSM3326366", "GSM3326367", "GSM3326368", "GSM3326369", "GSM3326370", "GSM3326371", "GSM3326372", "GSM3326373", "GSM3326374", "GSM3326375", "GSM3326376", "GSM3326377", "GSM3326378", "GSM3326379", "GSM3326380", "GSM3326381", "GSM3326382", "GSM3326383", "GSM3326384", "GSM3326385", "GSM3326386", "GSM3326387", "GSM3326388", "GSM3326389", "GSM3326390", "GSM3326391", "GSM3326392", "GSM3326393", "GSM3326394", "GSM3326395", "GSM3326396", "GSM3326397", "GSM3326398", "GSM3326399", "GSM3326400", "GSM3326401", "GSM3326402", "GSM3326403", "GSM3326404", "GSM3326405", "GSM3326406", "GSM3326407", "GSM3326408", "GSM3326409", "GSM3326410", "GSM3326411", "GSM3326412", "GSM3326413", "GSM3326414", "GSM3326415", "GSM3326416", "GSM3326417", "GSM3326418", "GSM3326419", "GSM3326420", "GSM3326421", "GSM3326422", "GSM3326423", "GSM3326424", "GSM3326425", "GSM3326426", "GSM3326427", "GSM3326428", "GSM3326429", "GSM3326430", "GSM3326431", "GSM3326432", "GSM3326433", "GSM3326434", "GSM3326435", "GSM3326436", "GSM3326437", "GSM3326438", "GSM3326439", "GSM3326440", "GSM3326441", "GSM3326442", "GSM3326443", "GSM3326444", "GSM3326445", "GSM3326446", "GSM3326447", "GSM3326448", "GSM3326449", "GSM3326450", "GSM3326451", "GSM3326452", "GSM3326453", "GSM3326454", "GSM3326455", "GSM3326456", "GSM3326457", "GSM3326458", "GSM3326459", "GSM3326460", "GSM3326461", "GSM3326462", "GSM3326463", "GSM3326464", "GSM3326465", "GSM3326466", "GSM3326467", "GSM3326468", "GSM3326469", "GSM3326470", "GSM3326471", "GSM3326472", "GSM3326473", "GSM3326474", "GSM3326475", "GSM3326476", "GSM3326477", "GSM3326478", "GSM3326479", "GSM3326480", "GSM3326481", "GSM3326482", "GSM3326483", "GSM3326484", "GSM3326485", "GSM3326486", "GSM3326487", "GSM3326488", "GSM3326489", "GSM3326490", "GSM3326491", "GSM3326492", "GSM3326493", "GSM3326494", "GSM3326495", "GSM3326496", "GSM3326497", "GSM3326498", "GSM3326499", "GSM3326500", "GSM3326501", "GSM3326502", "GSM3326503", "GSM3326504", "GSM3326505", "GSM3326506", "GSM3326507", "GSM3326508", "GSM3326509", "GSM3326510", "GSM3326511", "GSM3326512", "GSM3326513", "GSM3326514", "GSM3326515", "GSM3326516", "GSM3326517", "GSM3326518", "GSM3326519", "GSM3326520", "GSM3326521", "GSM3326522", "GSM3326523", "GSM3326524", "GSM3326525", "GSM3326526", "GSM3326527", "GSM3326528", "GSM3326529", "GSM3326530", "GSM3326531", "GSM3326532", "GSM3326533", "GSM3326534", "GSM3326535", "GSM3326536", "GSM3326537", "GSM3326538", "GSM3326539", "GSM3326540", "GSM3326541", "GSM3326542", "GSM3326543", "GSM3326544", "GSM3326545", "GSM3326546", "GSM3326547", "GSM3326548", "GSM3326549", "GSM3326550", "GSM3326551", "GSM3326552", "GSM3326553", "GSM3326554", "GSM3326555", "GSM3326556", "GSM3326557", "GSM3326558", "GSM3326559", "GSM3326560", "GSM3326561", "GSM3326562", "GSM3326563", "GSM3326564", "GSM3326565", "GSM3326566", "GSM3326567", "GSM3326568", "GSM3326569", "GSM3326570", "GSM3326571", "GSM3326572", "GSM3326573", "GSM3326574", "GSM3326575", "GSM3326576", "GSM3326577", "GSM3326578", "GSM3326579", "GSM3326580", "GSM3326581", "GSM3326582", "GSM3326583", "GSM3326584", "GSM3326585", "GSM3326586", "GSM3326587", "GSM3326588", "GSM3326589", "GSM3326590", "GSM3326591", "GSM3326592", "GSM3326593", "GSM3326594", "GSM3326595", "GSM3326596", "GSM3326597", "GSM3326598", "GSM3326599", "GSM3326600", "GSM3326601", "GSM3326602", "GSM3326603", "GSM3326604", "GSM3326605", "GSM3326606", "GSM3326607", "GSM3326608", "GSM3326609", "GSM3326610", "GSM3326611", "GSM3326612", "GSM3326613", "GSM3326614", "GSM3326615", "GSM3326616", "GSM3326617", "GSM3326618", "GSM3326619", "GSM3326620", "GSM3326621", "GSM3326622", "GSM3326623", "GSM3326624", "GSM3326625", "GSM3326626", "GSM3326627", "GSM3326628", "GSM3326629", "GSM3326630", "GSM3326631", "GSM3326632", "GSM3326633", "GSM3326634", "GSM3326635", "GSM3326636", "GSM3326637", "GSM3326638", "GSM3326639", "GSM3326640", "GSM3326641", "GSM3326642", "GSM3326643", "GSM3326644", "GSM3326645", "GSM3326646", "GSM3326647", "GSM3326648", "GSM3326649", "GSM3326650", "GSM3326651", "GSM3326652", "GSM3326653", "GSM3326654", "GSM3326655", "GSM3326656", "GSM3326657", "GSM3326658", "GSM3326659", "GSM3326660", "GSM3326661", "GSM3326662", "GSM3326663", "GSM3326664", "GSM3326665", "GSM3326666", "GSM3326667", "GSM3326668", "GSM3326669", "GSM3326670", "GSM3326671", "GSM3326672", "GSM3326673", "GSM3326674", "GSM3326675", "GSM3326676", "GSM3326677", "GSM3326678", "GSM3326679", "GSM3326680", "GSM3326681", "GSM3326682", "GSM3326683", "GSM3326684", "GSM3326685", "GSM3326686", "GSM3326687", "GSM3326688", "GSM3326689", "GSM3326690", "GSM3326691", "GSM3326692", "GSM3326693", "GSM3326694", "GSM3326695", "GSM3326696", "GSM3326697", "GSM3326698", "GSM3326699", "GSM3326700", "GSM3326701", "GSM3326702", "GSM3326703", "GSM3326704", "GSM3326705", "GSM3326706", "GSM3326707", "GSM3326708", "GSM3326709", "GSM3326710", "GSM3326711", "GSM3326712", "GSM3326713", "GSM3326714", "GSM3326715", "GSM3326716", "GSM3326717", "GSM3326718", "GSM3326719", "GSM3326720", "GSM3326721", "GSM3326722", "GSM3326723", "GSM3326724", "GSM3326725", "GSM3326726", "GSM3326727", "GSM3326728", "GSM3326729", "GSM3326730", "GSM3326731", "GSM3326732", "GSM3326733", "GSM3326734", "GSM3326735", "GSM3326736", "GSM3326737", "GSM3326738", "GSM3326739", "GSM3326740", "GSM3326741", "GSM3326742", "GSM3326743", "GSM3326744", "GSM3326745", "GSM3326746", "GSM3326747", "GSM3326748", "GSM3326749", "GSM3326750", "GSM3326751", "GSM3326752", "GSM3326753", "GSM3326754", "GSM3326755", "GSM3326756", "GSM3326757", "GSM3326758", "GSM3326759", "GSM3326760", "GSM3326761", "GSM3326762", "GSM3326763", "GSM3326764", "GSM3326765", "GSM3326766", "GSM3326767", "GSM3326768", "GSM3326769", "GSM3326770", "GSM3326771", "GSM3326772", "GSM3326773", "GSM3326774", "GSM3326775", "GSM3326776", "GSM3326777", "GSM3326778", "GSM3326779", "GSM3326780", "GSM3326781", "GSM3326782", "GSM3326783", "GSM3326784", "GSM3326785", "GSM3326786", "GSM3326787", "GSM3326788", "GSM3326789", "GSM3326790", "GSM3326791", "GSM3326792", "GSM3326793", "GSM3326794", "GSM3326795", "GSM3326796", "GSM3326797", "GSM3326798", "GSM3326799", "GSM3326800", "GSM3326801", "GSM3326802", "GSM3326803", "GSM3326804", "GSM3326805", "GSM3326806", "GSM3326807", "GSM3326808", "GSM3326809", "GSM3326810", "GSM3326811", "GSM3326812", "GSM3326813", "GSM3326814", "GSM3326815", "GSM3326816", "GSM3326817", "GSM3326818", "GSM3326819", "GSM3326820", "GSM3326821", "GSM3326822", "GSM3326823", "GSM3326824", "GSM3326825", "GSM3326826", "GSM3326827", "GSM3326828", "GSM3326829", "GSM3326830", "GSM3326831", "GSM3326832", "GSM3326833", "GSM3326834", "GSM3326835", "GSM3326836", "GSM3326837", "GSM3326838", "GSM3326839", "GSM3326840", "GSM3326841", "GSM3326842", "GSM3326843", "GSM3326844", "GSM3326845", "GSM3326846", "GSM3326847", "GSM3326848", "GSM3326849", "GSM3326850", "GSM3326851", "GSM3326852", "GSM3326853", "GSM3326854", "GSM3326855", "GSM3326856", "GSM3326857", "GSM3326858", "GSM3326859", "GSM3326860", "GSM3326861", "GSM3326862", "GSM3326863", "GSM3326864", "GSM3326865", "GSM3326866", "GSM3326867", "GSM3326868", "GSM3326869", "GSM3326870", "GSM3326871", "GSM3326872", "GSM3326873", "GSM3326874", "GSM3326875", "GSM3326876", "GSM3326877", "GSM3326878", "GSM3326879", "GSM3326880", "GSM3326881", "GSM3326882", "GSM3326883", "GSM3326884", "GSM3326885", "GSM3326886", "GSM3326887", "GSM3326888", "GSM3326889", "GSM3326890", "GSM3326891", "GSM3326892", "GSM3326893", "GSM3326894", "GSM3326895", "GSM3326896", "GSM3326897", "GSM3326898", "GSM3326899", "GSM3326900", "GSM3326901", "GSM3326902", "GSM3326903", "GSM3326904", "GSM3326905", "GSM3326906", "GSM3326907", "GSM3326908", "GSM3326909", "GSM3326910", "GSM3326911", "GSM3326912", "GSM3326913", "GSM3326914", "GSM3326915", "GSM3326916", "GSM3326917", "GSM3326918", "GSM3326919", "GSM3326920", "GSM3326921", "GSM3326922", "GSM3326923", "GSM3326924", "GSM3326925", "GSM3326926", "GSM3326927", "GSM3326928", "GSM3326929", "GSM3326930", "GSM3326931", "GSM3326932", "GSM3326933", "GSM3326934", "GSM3326935", "GSM3326936", "GSM3326937", "GSM3326938", "GSM3326939", "GSM3326940", "GSM3326941", "GSM3326942", "GSM3326943", "GSM3326944", "GSM3326945", "GSM3326946", "GSM3326947", "GSM3326948", "GSM3326949", "GSM3326950", "GSM3326951", "GSM3326952", "GSM3326953", "GSM3326954", "GSM3326955", "GSM3326956", "GSM3326957", "GSM3326958", "GSM3326959", "GSM3326960", "GSM3326961", "GSM3326962", "GSM3326963", "GSM3326964", "GSM3326965", "GSM3326966", "GSM3326967", "GSM3326968", "GSM3326969", "GSM3326970", "GSM3326971", "GSM3326972", "GSM3326973", "GSM3326974", "GSM3326975", "GSM3326976", "GSM3326977", "GSM3326978", "GSM3326979", "GSM3326980", "GSM3326981", "GSM3326982", "GSM3326983", "GSM3326984", "GSM3326985", "GSM3326986", "GSM3326987", "GSM3326988", "GSM3326989", "GSM3326990", "GSM3326991", "GSM3326992", "GSM3326993", "GSM3326994", "GSM3326995", "GSM3326996", "GSM3326997", "GSM3326998", "GSM3326999", "GSM3327000", "GSM3327001", "GSM3327002", "GSM3327003", "GSM3327004", "GSM3327005", "GSM3327006", "GSM3327007", "GSM3327008", "GSM3327009", "GSM3327010", "GSM3327011", "GSM3327012", "GSM3327013", "GSM3327014", "GSM3327015", "GSM3327016", "GSM3327017", "GSM3327018", "GSM3327019", "GSM3327020", "GSM3327021", "GSM3327022", "GSM3327023", "GSM3327024", "GSM3327025", "GSM3327026", "GSM3327027", "GSM3327028", "GSM3327029", "GSM3327030", "GSM3327031", "GSM3327032", "GSM3327033", "GSM3327034", "GSM3327035", "GSM3327036", "GSM3327037", "GSM3327038", "GSM3327039", "GSM3327040", "GSM3327041", "GSM3327042", "GSM3327043", "GSM3327044", "GSM3327045", "GSM3327046", "GSM3327047", "GSM3327048", "GSM3327049", "GSM3327050", "GSM3327051", "GSM3327052", "GSM3327053", "GSM3327054", "GSM3327055", "GSM3327056", "GSM3327057", "GSM3327058", "GSM3327059", "GSM3327060", "GSM3327061", "GSM3327062", "GSM3327063", "GSM3327064", "GSM3327065", "GSM3327066", "GSM3327067", "GSM3327068", "GSM3327069", "GSM3327070", "GSM3327071", "GSM3327072", "GSM3327073", "GSM3327074", "GSM3327075", "GSM3327076", "GSM3327077", "GSM3327078", "GSM3327079", "GSM3327080", "GSM3327081", "GSM3327082", "GSM3327083", "GSM3327084", "GSM3327085", "GSM3327086", "GSM3327087", "GSM3327088", "GSM3327089", "GSM3327090", "GSM3327091", "GSM3327092", "GSM3327093", "GSM3327094", "GSM3327095", "GSM3327096", "GSM3327097", "GSM3327098", "GSM3327099", "GSM3327100", "GSM3327101", "GSM3327102", "GSM3327103", "GSM3327104", "GSM3327105", "GSM3327106", "GSM3327107", "GSM3327108", "GSM3327109", "GSM3327110", "GSM3327111", "GSM3327112", "GSM3327113", "GSM3327114", "GSM3327115", "GSM3327116", "GSM3327117", "GSM3327118", "GSM3327119", "GSM3327120", "GSM3327121", "GSM3327122", "GSM3327123", "GSM3327124", "GSM3327125", "GSM3327126", "GSM3327127", "GSM3327128", "GSM3327129", "GSM3327130", "GSM3327131", "GSM3327132", "GSM3327133", "GSM3327134", "GSM3327135", "GSM3327136", "GSM3327137", "GSM3327138", "GSM3327139", "GSM3327140", "GSM3327141", "GSM3327142", "GSM3327143", "GSM3327144", "GSM3327145", "GSM3327146", "GSM3327147", "GSM3327148", "GSM3327149", "GSM3327150", "GSM3327151", "GSM3327152", "GSM3327153", "GSM3327154", "GSM3327155", "GSM3327156", "GSM3327157", "GSM3327158", "GSM3327159", "GSM3327160", "GSM3327161", "GSM3327162", "GSM3327163", "GSM3327164", "GSM3327165", "GSM3327166", "GSM3327167", "GSM3327168", "GSM3327169", "GSM3327170", "GSM3327171", "GSM3327172", "GSM3327173", "GSM3327174", "GSM3327175", "GSM3327176", "GSM3327177", "GSM3327178", "GSM3327179", "GSM3327180", "GSM3327181", "GSM3327182", "GSM3327183", "GSM3327184", "GSM3327185", "GSM3327186", "GSM3327187", "GSM3327188", "GSM3327189", "GSM3327190", "GSM3327191", "GSM3327192", "GSM3327193", "GSM3327194", "GSM3327195", "GSM3327196", "GSM3327197", "GSM3327198", "GSM3327199", "GSM3327200", "GSM3327201", "GSM3327202", "GSM3327203", "GSM3327204", "GSM3327205", "GSM3327206", "GSM3327207", "GSM3327208", "GSM3327209", "GSM3327210", "GSM3327211", "GSM3327212", "GSM3327213", "GSM3327214", "GSM3327215", "GSM3327216", "GSM3327217", "GSM3327218", "GSM3327219", "GSM3327220", "GSM3327221", "GSM3327222", "GSM3327223", "GSM3327224", "GSM3327225", "GSM3327226", "GSM3327227", "GSM3327228", "GSM3327229", "GSM3327230", "GSM3327231", "GSM3327232", "GSM3327233", "GSM3327234", "GSM3327235", "GSM3327236", "GSM3327237", "GSM3327238", "GSM3327239", "GSM3327240", "GSM3327241", "GSM3327242", "GSM3327243", "GSM3327244", "GSM3327245", "GSM3327246", "GSM3327247", "GSM3327248", "GSM3327249", "GSM3327250", "GSM3327251", "GSM3327252", "GSM3327253", "GSM3327254", "GSM3327255", "GSM3327256", "GSM3327257", "GSM3327258", "GSM3327259", "GSM3327260", "GSM3327261", "GSM3327262", "GSM3327263", "GSM3327264", "GSM3327265", "GSM3327266", "GSM3327267", "GSM3327268", "GSM3327269", "GSM3327270", "GSM3327271", "GSM3327272", "GSM3327273", "GSM3327274", "GSM3327275", "GSM3327276", "GSM3327277", "GSM3327278", "GSM3327279", "GSM3327280", "GSM3327281", "GSM3327282", "GSM3327283", "GSM3327284", "GSM3327285", "GSM3327286", "GSM3327287", "GSM3327288", "GSM3327289", "GSM3327290", "GSM3327291", "GSM3327292", "GSM3327293", "GSM3327294", "GSM3327295", "GSM3327296", "GSM3327297", "GSM3327298", "GSM3327299", "GSM3327300", "GSM3327301", "GSM3327302", "GSM3327303", "GSM3327304", "GSM3327305", "GSM3327306", "GSM3327307", "GSM3327308", "GSM3327309", "GSM3327310", "GSM3327311", "GSM3327312", "GSM3327313", "GSM3327314", "GSM3327315", "GSM3327316", "GSM3327317", "GSM3327318", "GSM3327319", "GSM3327320", "GSM3327321", "GSM3327322", "GSM3327323", "GSM3327324", "GSM3327325", "GSM3327326", "GSM3327327", "GSM3327328", "GSM3327329", "GSM3327330", "GSM3327331", "GSM3327332", "GSM3327333", "GSM3327334", "GSM3327335", "GSM3327336", "GSM3327337", "GSM3327338", "GSM3327339", "GSM3327340", "GSM3327341", "GSM3327342", "GSM3327343", "GSM3327344", "GSM3327345", "GSM3327346", "GSM3327347", "GSM3327348", "GSM3327349", "GSM3327350", "GSM3327351", "GSM3327352", "GSM3327353", "GSM3327354", "GSM3327355", "GSM3327356", "GSM3327357", "GSM3327358", "GSM3327359", "GSM3327360", "GSM3327361", "GSM3327362", "GSM3327363", "GSM3327364", "GSM3327365", "GSM3327366", "GSM3327367", "GSM3327368", "GSM3327369", "GSM3327370", "GSM3327371", "GSM3327372", "GSM3327373", "GSM3327374", "GSM3327375", "GSM3327376", "GSM3327377", "GSM3327378", "GSM3327379", "GSM3327380", "GSM3327381", "GSM3327382", "GSM3327383", "GSM3327384", "GSM3327385", "GSM3327386", "GSM3327387", "GSM3327388", "GSM3327389", "GSM3327390", "GSM3327391", "GSM3327392", "GSM3327393", "GSM3327394", "GSM3327395", "GSM3327396", "GSM3327397", "GSM3327398", "GSM3327399", "GSM3327400", "GSM3327401", "GSM3327402", "GSM3327403", "GSM3327404", "GSM3327405", "GSM3327406", "GSM3327407", "GSM3327408", "GSM3327409", "GSM3327410", "GSM3327411", "GSM3327412", "GSM3327413", "GSM3327414", "GSM3327415", "GSM3327416", "GSM3327417", "GSM3327418", "GSM3327419", "GSM3327420", "GSM3327421", "GSM3327422", "GSM3327423", "GSM3327424", "GSM3327425", "GSM3327426", "GSM3327427", "GSM3327428", "GSM3327429", "GSM3327430", "GSM3327431", "GSM3327432", "GSM3327433", "GSM3327434", "GSM3327435", "GSM3327436", "GSM3327437", "GSM3327438", "GSM3327439", "GSM3327440", "GSM3327441", "GSM3327442", "GSM3327443", "GSM3327444", "GSM3327445", "GSM3327446", "GSM3327447", "GSM3327448", "GSM3327449", "GSM3327450", "GSM3327451", "GSM3327452", "GSM3327453", "GSM3327454", "GSM3327455", "GSM3327456", "GSM3327457", "GSM3327458", "GSM3327459", "GSM3327460", "GSM3327461", "GSM3327462", "GSM3327463", "GSM3327464", "GSM3327465", "GSM3327466", "GSM3327467", "GSM3327468", "GSM3327469", "GSM3327470", "GSM3327471", "GSM3327472", "GSM3327473", "GSM3327474", "GSM3327475", "GSM3327476", "GSM3327477", "GSM3327478", "GSM3327479", "GSM3327480", "GSM3327481", "GSM3327482", "GSM3327483", "GSM3327484", "GSM3327485", "GSM3327486", "GSM3327487", "GSM3327488", "GSM3327489", "GSM3327490", "GSM3327491", "GSM3327492", "GSM3327493", "GSM3327494", "GSM3327495", "GSM3327496", "GSM3327497", "GSM3327498", "GSM3327499", "GSM3327500", "GSM3327501", "GSM3327502", "GSM3327503", "GSM3327504", "GSM3327505", "GSM3327506", "GSM3327507", "GSM3327508", "GSM3327509", "GSM3327510", "GSM3327511", "GSM3327512", "GSM3327513", "GSM3327514", "GSM3327515", "GSM3327516", "GSM3327517", "GSM3327518", "GSM3327519", "GSM3327520", "GSM3327521", "GSM3327522", "GSM3327523", "GSM3327524", "GSM3327525", "GSM3327526", "GSM3327527", "GSM3327528", "GSM3327529", "GSM3327530", "GSM3327531", "GSM3327532", "GSM3327533", "GSM3327534", "GSM3327535", "GSM3327536", "GSM3327537", "GSM3327538", "GSM3327539", "GSM3327540", "GSM3327541", "GSM3327542", "GSM3327543", "GSM3327544", "GSM3327545", "GSM3327546", "GSM3327547", "GSM3327548", "GSM3327549", "GSM3327550", "GSM3327551", "GSM3327552", "GSM3327553", "GSM3327554", "GSM3327555", "GSM3327556", "GSM3327557", "GSM3327558", "GSM3327559", "GSM3327560", "GSM3327561", "GSM3327562", "GSM3327563", "GSM3327564", "GSM3327565", "GSM3327566", "GSM3327567", "GSM3327568", "GSM3327569", "GSM3327570", "GSM3327571", "GSM3327572", "GSM3327573", "GSM3327574", "GSM3327575", "GSM3327576", "GSM3327577", "GSM3327578", "GSM3327579", "GSM3327580", "GSM3327581", "GSM3327582", "GSM3327583", "GSM3327584", "GSM3327585", "GSM3327586", "GSM3327587", "GSM3327588", "GSM3327589", "GSM3327590", "GSM3327591", "GSM3327592", "GSM3327593", "GSM3327594", "GSM3327595", "GSM3327596", "GSM3327597", "GSM3327598", "GSM3327599", "GSM3327600", "GSM3327601", "GSM3327602", "GSM3327603", "GSM3327604", "GSM3327605", "GSM3327606", "GSM3327607", "GSM3327608", "GSM3327609", "GSM3327610", "GSM3327611", "GSM3327612", "GSM3327613", "GSM3327614", "GSM3327615", "GSM3327616", "GSM3327617", "GSM3327618", "GSM3327619", "GSM3327620", "GSM3327621", "GSM3327622", "GSM3327623", "GSM3327624", "GSM3327625", "GSM3327626", "GSM3327627", "GSM3327628", "GSM3327629", "GSM3327630", "GSM3327631", "GSM3327632", "GSM3327633", "GSM3327634", "GSM3327635", "GSM3327636", "GSM3327637", "GSM3327638", "GSM3327639", "GSM3327640", "GSM3327641", "GSM3327642", "GSM3327643", "GSM3327644", "GSM3327645", "GSM3327646", "GSM3327647", "GSM3327648", "GSM3327649", "GSM3327650", "GSM3327651", "GSM3327652", "GSM3327653", "GSM3327654", "GSM3327655", "GSM3327656", "GSM3327657", "GSM3327658", "GSM3327659", "GSM3327660", "GSM3327661", "GSM3327662", "GSM3327663", "GSM3327664", "GSM3327665", "GSM3327666", "GSM3327667", "GSM3327668", "GSM3327669", "GSM3327670", "GSM3327671", "GSM3327672", "GSM3327673", "GSM3327674", "GSM3327675", "GSM3327676", "GSM3327677", "GSM3327678", "GSM3327679", "GSM3327680", "GSM3327681", "GSM3327682", "GSM3327683", "GSM3327684", "GSM3327685", "GSM3327686", "GSM3327687", "GSM3327688", "GSM3327689", "GSM3327690", "GSM3327691", "GSM3327692", "GSM3327693", "GSM3327694", "GSM3327695", "GSM3327696", "GSM3327697", "GSM3327698", "GSM3327699", "GSM3327700", "GSM3327701", "GSM3327702", "GSM3327703", "GSM3327704", "GSM3327705"], "sample_count": 1534, "group_sizes": null, "group_sizes_basis": null, "platform": "9052", "taxon": "Homo sapiens", "title": "Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq [RNA-Seq]", "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:GSE161529", "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=GSE161529", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE161529", "version": null, "note": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4909253", "GSM4909254", "GSM4909255", "GSM4909256", "GSM4909257", "GSM4909258", "GSM4909259", "GSM4909260", "GSM4909261", "GSM4909262", "GSM4909263", "GSM4909264", "GSM4909265", "GSM4909266", "GSM4909267", "GSM4909268", "GSM4909269", "GSM4909270", "GSM4909271", "GSM4909272", "GSM4909273", "GSM4909274", "GSM4909275", "GSM4909276", "GSM4909277", "GSM4909278", "GSM4909279", "GSM4909280", "GSM4909281", "GSM4909282", "GSM4909283", "GSM4909284", "GSM4909285", "GSM4909286", "GSM4909287", "GSM4909288", "GSM4909289", "GSM4909290", "GSM4909291", "GSM4909292", "GSM4909293", "GSM4909294", "GSM4909295", "GSM4909296", "GSM4909297", "GSM4909298", "GSM4909299", "GSM4909300", "GSM4909301", "GSM4909302", "GSM4909303", "GSM4909304", "GSM4909305", "GSM4909306", "GSM4909307", "GSM4909308", "GSM4909309", "GSM4909310", "GSM4909311", "GSM4909312", "GSM4909313", "GSM4909314", "GSM4909315", "GSM4909316", "GSM4909317", "GSM4909318", "GSM4909319", "GSM4909320", "GSM4909321"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE76124", "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=GSE76124", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76124", "version": null, "note": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "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"], "sample_count": 198, "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 (198 TNBC tumors)", "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:GSE103091 not downloaded", "asset:data:geo:GSE103091 licence not read", "asset:data:geo:GSE118389 not downloaded", "asset:data:geo:GSE118389 licence not read", "asset:data:geo:GSE161529 not downloaded", "asset:data:geo:GSE161529 licence not read", "asset:data:geo:GSE76124 not downloaded", "asset:data:geo:GSE76124 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Time-dependent ROC curves were used to study the predictive power of the prognostic model"}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "KM"}}, {"id": "method-3", "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-4", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.8, "band": "high", "quote": "Decision Curve Analysis"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: roc."}, "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": ["GSE103091", "GSE76124", "GSE118389", "GSE161529"], "resolved_accessions": ["GSE103091", "GSE76124", "GSE118389", "GSE161529"], "statements": ["The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git"], "basis": "The paper names GSE103091, GSE76124, GSE118389, GSE161529 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "assets": ["source:pmid:34900411", "data:geo:GSE103091"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE103091"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:11:16Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16646, "completion_tokens": 2598, "cached_tokens": 264}}, "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:34900411", "type": "paper", "label": "pmid:34900411"}, {"id": "source:pmid:34900411", "type": "manuscript", "label": "PMID 34900411 full text"}, {"id": "data:geo:GSE103091", "type": "dataset", "label": "GEO GSE103091"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34900411", "type": "paper", "label": "pmid:34900411"}, {"id": "source:pmid:34900411", "type": "manuscript", "label": "PMID 34900411 full text"}, {"id": "data:geo:GSE103091", "type": "dataset", "label": "GEO GSE103091"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34900411", "type": "extraction", "used": ["source:pmid:34900411"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE103091", "type": "accession_resolution", "used": ["data:geo:GSE103091"], "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:34900411", "parent_hash": "sha256:461913423fc765227f162ec1519f05523af06f39205f21e254c51f5d7de4a386", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE103091 licence not read", "asset:data:geo:GSE103091 not downloaded", "asset:data:geo:GSE118389 licence not read", "asset:data:geo:GSE118389 not downloaded", "asset:data:geo:GSE161529 licence not read", "asset:data:geo:GSE161529 not downloaded", "asset:data:geo:GSE76124 licence not read", "asset:data:geo:GSE76124 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "methylation_array", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["statistical analysis (Bindea et al., 2013). EPIC (http://epic.gfellerlab.org/) can analyze th", "analysis (Bindea et al., 2013). EPIC (http://epic.gfellerlab.org/) can analyze the infiltratio", "n analysis of different modules in WGCNA and EPIC immune cell score results10.7717/peerj.12383"], "order_basis": "paper_text_order:4786", "id": "assay:1"}, {"role": "analysis", "definition_id": "diagnostic_evaluation", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Time-dependent ROC curves were used to study the predictive power of the prognostic model"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:49:14+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}