← All .science files
pmid:39418248
Establishment of a tumor-associated fibroblast associated gene score based on scRNA-seq to predict prognosis in patients with triple-negative breast cancer.
Hao Yu · Ziqi Peng · Xing Li · Yiqi Zhang
PloS one · 2024 doi:10.1371/journal.pone.0311801
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 4 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
[2] object · 6 fields
target object · 4 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 238 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 1534 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 12 items
gaps array · 6 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 6 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 1 item
[0] object · 8 fields
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 3 items
resolved_accessions array · 3 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 10 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39418248", "kind": "science-record", "revision": 3, "content_hash": "sha256:56c7d68c3856139eda336a5a34c024a096c77378629f0b13009aa09bb99bd2b3", "created_at": "2026-11-01T20:29:39Z", "updated_at": "2026-11-01T22:12:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment of a tumor-associated fibroblast associated gene score based on scRNA-seq to predict prognosis in patients with triple-negative breast cancer.", "doi": "10.1371/journal.pone.0311801", "pmid": "39418248", "authors": ["Hao Yu", "Ziqi Peng", "Xing Li", "Yiqi Zhang"], "journal": "PloS one", "year": 2024, "abstract": "The tumor microenvironment (TME) is emerging as a tool for the development of improved patient prognosis and the development of novel antitumor drugs. As the most important stromal cells in the tumor microenvironment, cancer-associated fibroblasts (CAFs) play an important role in the development of TNBC. The rise of single-cell sequencing technology has facilitated our study of the various cell types in TME. In this study, we interpreted the heterogeneity of TNBCs from the perspective of tumor-associated fibroblasts in the tumor microenvironment based on the TNBC single-cell sequencing dataset GSE118389, in the hope of providing help for individualised treatment. Combining the TCGA database and the GSE103091 dataset, four genes associated with CAFs in TNBC (CERCAM, KLF10, ECM1,HGF) were identified using the R package Seurat as well as correlation consensus clustering analysis. Meanwhile, qRT-PCR, WB and IHC experiments confirmed their expression in TNBC. Based on these genes, CAFs Score was established and validated to correlate with the prognosis of patients with TNBC, with patients in the high score group surviving significantly worse than those in the low score group (P<0.001). In addition, there were significant differences in immune cell infiltration and expression of immune checkpoints between the high and low scoring groups. Compared to Stage I & II, the CAFs Score was higher in Stage III & IV TNBC patients (P = 0.043) and higher in N1-3 TNBC patients than in N0 TNBC patients (P = 0.035). EMT scores were higher within the high CAFs Score group (P = 1.4e-11) and there was a positive correlation between Stemness Score and CAFs Score (R = 0.61, P = 3.6e-09). Drug sensitivity analysis combining the GSE128099 showed a higher sensitivity to Gemcitabine in the low CAFs Score group (P = 0.0048). We speculate that these four CAFs-related genes are likely to be involved in regulating gemcitabine resistance in TNBC patients.", "claims": [{"id": "claim-method", "statement": "Expression data of marker genes were extracted from TCGA-TNBC, and univariate cox regression analysis was performed based on patients’ total survival time, a total of 40 overall survival (OS) related genes were identified (Fig 3A).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39418248", "locator": "sections[17] \"3.3 Identification of CAFs subtypes in TCGA-TNBC\" paragraph 2", "quote": "Expression data of marker genes were extracted from TCGA-TNBC, and univariate cox regression analysis was performed based on patients’ total survival time, a total of 40 overall survival (OS) related genes were identified (Fig 3A)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39418248", "locator": "sections[27] \"Data Availability\" paragraph 2", "quote": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Based on these genes, CAFs Score was established and validated to correlate with the prognosis of patients with TNBC, with patients in the high score group surviving significantly worse than those in the low score group (P<0.001).", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Based on these genes, CAFs Score was established and validated to correlate with the prognosis of patients with TNBC, with patients in the high score group surviving significantly worse than those in the low score group (P<0.001)."}, "evidence": [{"asset": "source:pmid:39418248", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Based on these genes, CAFs Score was established and validated to correlate with the prognosis of patients with TNBC, with patients in the high score group surviving significantly worse than those in the low score group (P<0.001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Based on these genes, CAFs Score was established and validated to correlate with the prognosis of patients with TNBC, with patients in the high score group surviving significantly worse than those in the low score group (P<0.001).", "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:39418248"], "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:39418248", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0311801", "sha256": "sha256:751f1f0ee5be416aae9018cbe7a65a8a0be7363bb393401b3e0e81f589696863", "bytes": 55084, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0311801", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11486389", "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": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part.", "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": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part.", "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:GSE128099", "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=GSE128099", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE128099", "version": null, "note": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3664912", "GSM3664913", "GSM3664914", "GSM3664915", "GSM3664916", "GSM3664917", "GSM3664918", "GSM3664919", "GSM3664920", "GSM3664921", "GSM3664922", "GSM3664923"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "RNA-seq of shE4F1 or shCTRL SUM159 triple negative breast cancer cell line treated or not with Gemcitabine", "resolution_checked_at": "2026-11-01T20:16:08Z", "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:GSE128099 not downloaded", "asset:data:geo:GSE128099 licence not read"]}, "analysis": {"state": "complete", "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": 1.0, "band": "verbatim", "quote": "Expression data of marker genes were extracted from TCGA-TNBC, and univariate cox regression analysis was performed based on patients’ total survival time, a total of 40 overall survival (OS) related genes were identified (Fig 3A)."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-3", "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": 0.8, "band": "high", "quote": "ROC analysis"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 0.001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["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": ["GSE118389", "GSE103091", "GSE128099"], "resolved_accessions": ["GSE118389", "GSE103091", "GSE128099"], "statements": ["We have added the direct link of GSE118389, GSE103091, GSE128099 and TCGA database in material part."], "basis": "The paper names GSE118389, GSE103091, GSE128099 in 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:39418248", "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": "2026-11-01T19:35:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15414, "completion_tokens": 2604, "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:39418248", "type": "paper", "label": "pmid:39418248"}, {"id": "source:pmid:39418248", "type": "manuscript", "label": "PMID 39418248 full text"}, {"id": "data:geo:GSE103091", "type": "dataset", "label": "GEO GSE103091"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39418248", "type": "paper", "label": "pmid:39418248"}, {"id": "source:pmid:39418248", "type": "manuscript", "label": "PMID 39418248 full text"}, {"id": "data:geo:GSE103091", "type": "dataset", "label": "GEO GSE103091"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39418248", "type": "extraction", "used": ["source:pmid:39418248"], "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:39418248", "parent_hash": "sha256:3b583c7d042893fb9fa29afe3a26d38a24b69d8e779cea95613b86db5b6c9c45", "fork_of": null, "generation": 2}, "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:GSE128099 licence not read", "asset:data:geo:GSE128099 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ed fibroblast associated gene score based on scRNA-seq to predict prognosis in patients with triple"], "order_basis": "paper_text_order:33", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["stering analysis. Meanwhile, qRT-PCR, WB and IHC experiments confirmed their expression in TN"], "order_basis": "paper_text_order:1029", "id": "assay:2"}, {"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": 1.0, "evidence": ["Expression data of marker genes were extracted from TCGA-TNBC, and univariate cox regression analysis was performed based on patients’ total survival time, a total of 40 overall survival (OS) related genes were identified (Fig 3A)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}